3D-Match
Bacterial Genome Explorer
BESTORF
BestPal
BPROM
CpGFinder
CTL epitope-Finder
CYS_REC
EST_map
Fex
FGENES
FGENES-M
FGENESB
FGENESH 2014
FGENESH 2013
FGENESH 2012
FGENESH 2011
FGENESH 2010
FGENESH 2009
FGENESH 2008
FGENESH 2007
FGENESH 2006
FGENESH 2005
FGENESH 2002-2004
FGENESH_GC
FGENESH-M
FGENESH+
FGENESH++
FGENESH-C
FGENESH-2
FGENESH++C
FGENESV, FGENESV0
FindMiRNA
FindTerm
FoldRNA
FPROM
FSPLICE
Genome Comparison Browser
Genome Explorer
GetAtoms
Human-mouse synteny
Human-mouse-rat synteny
MaliN
MaliP
MolQuest
NNSSP
NSITE
NSITE-PL
NSITEM
OligoZip
PATTERN
Pdisorder
PlantProm
POLYAH
PROMH
PROTCOMP
PROT_MAP
PSITE
PSSFinder
Rat-mouse synteny
RegSite
RNASPL
SCAN2
ScanWM-P
SPL
SPLM
SPLICEDB
SSP
SSPAL
TSSG
TSSP
TSSW
Various programs

FGENESH 2014

International Biodeterioration & Biodegradation, 93, 186-194.
2014, 93, 186-194. DOI: 10.1016/j.ibiod.2014.06.001

Purification and characterization of a thermotolerant laccase isoform in Trametes trogii strain and its potential in dye decolorization

Yan J. et al.,
a Biotechnology Research Center of Life Science and Technology College, Kunming University of Science and Technology, Kunming Yunnan 650500, PR China b College of Life Science, the Southwest Forest University, Kunming Yunnan 650224, PR China

... The gene structure and amino acid sequences of full laccase were predicted and analyzed with Soft Berry-FGENSH/HMM-based gene structure prediction (http://linux1.softberry.com/ berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...


Tree Genetics & Genomes
2014, 10(2), 251-260. DOI: 10.1007/s11295-013-0678-9

Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance

Schouten H. J. et al.,
1. Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands 2. Inova Fruit, P.O. Box 222, 4190 CE, Geldermalsen, The Netherlands

... 2010b) was copied from the NCBI database (accession number GU295057.1). The Vr2-A, Vr2-B, and Vr2-C amino acid sequences in GMAL 2473 were predicted by means of the publicly available software FGENESH from SoftBerry. ...


PloS one
2014, 9(4), e93560. DOI: 10.1371/journal.pone.0093560

Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation

Park Y. J. et al.,
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea; Macrogen Inc., Seoul, Republic of Korea

... Gene identification was carried out using several methods, including ab initio gene structure prediction (Fgenesh; http://www.softberry.com), a homology-based approach (Fgenesh+; http://www.softberry.com), and transcriptome-based gene identification (Cufflinks; http://cufflinks ..


Cellular signalling
2014, 26(6), 1155-1165. DOI: 10.1016/j.cellsig.2014.02.003

Mature miR-183, negatively regulated by transcription factor GATA3, promotes 3T3-L1 adipogenesis through inhibition of the canonical Wnt/b -catenin signaling pathway by targeting LRP6

Chen C. et al.,
a Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China

... BDGP (http://www.fruitfly.org/seq_tools/promoter.html) and SoftBerry (http://linux1.softberry.com/ berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) computer programs were utilized to analyze miR-183 gene structure, including TSS, CDS, and polyA signal. ...


Euphytica
2014, 196(3), 341-348. DOI: 10.1007/s10681-013-1037-5

Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)

Yang X et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Minhang District, Shanghai, 200240, China 2. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, 201602, China

... (Voorrips 2002 ). Gene prediction in the target genomic DNA regions was performed using the program FGENESH (Salamov and Solovyev 2000 ) (http://?linux1.?softberry.? com/?), and the results were checked manually. Results. ...


Molecular Breeding
2014, 1-13. DOI: 10.1007/s11032-014-0088-1

Fine genetic mapping of a locus controlling short internode length in melon (Cucumis melo L.)

Hwang J. et al.,
1. Department of Horticultural Bioscience, Pusan National University, Miryang, 627-706, Republic of Korea 2. Gyeongnam Agricultural Research and Extension Services, Jinju, 663-985, Republic of Korea

... market type cucumber inbred line “9930” (Li et al. 2011b ) were determined using FGENESH software (Softberry Inc., Mount Kisco NY, USA; http://?sunl.?softberry.? com/?). Primer pairs were designed to amplify these exon ...


Fungal biology
2014, 118(2), 228-241. DOI: 10.1016/j.funbio.2013.12.001

The Podosphaera fusca TUB2 gene, a molecular “Swiss Army knife” with multiple applications in powdery mildew research

Vela-Corcia, D., Bellon-Gomez, D., Lopez-Ruiz, F., Tores, J. A., & Perez-Garcia, A.
a Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” - Universidad de Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Departamento de Microbiologia, Universidad de Malaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Malaga, Spain b Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” - Universidad de Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Estacion Experimental “La Mayora”, 29750 Algarrobo-Costa, Malaga, Spain

... Potential open reading frames (ORFs), introns, and exons were predicted using FGENESH software from SoftBerry (http://linux1.softberry.com/berry.phtml). Amino acid alignments were performed with the CLC Main Workbench (Aarhus). ...


Gene
2014, 534(2), 204-217. DOI: 10.1016/j.gene.2013.10.058

Genomic organization, sequence characterization and expression analysis of Tenebrio molitor apolipophorin-III in response to an intracellular pathogen, Listeria monocytogenes

Noh J. Y. et al.,
a Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea b Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City 336-745 Republic of Korea

... sequencing method (see above). The fosmid library sequence information was used for predicting TmapoLp-III gene architecture using FGENESH 2.6 software from Softberry (http://linux1.softberry.com/berry.phtml/). The sequence of ...


Developmental & Comparative Immunology
2014, 46(2), 208-221. DOI: 10.1016/j.dci.2014.04.009

Gene structure, cDNA characterization and RNAi-based functional analysis of a myeloid differentiation factor 88 homolog in Tenebrio molitor larvae exposed to Staphylococcus aureus infection

Patnaik B. B. et al.,
a Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea b Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City 336-745, Republic of Korea

... sequencing method (see above). 2.4. Sequence analysis. The fosmid clone corresponding to TmMyD88 was analyzed using the FGENESH 2.6 program at Softberry (http://linux1.softberry.com/berry.phtml/). The 5?-flanking ...


The ScientificWorld Journal
Volume 2014, Article ID 619746, 7 pages DOI: /10.1155/2014/619746

Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism.

Qiu, C., Yan, W., Deng, W., Song, B., Li, T.
1 Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, State Key Laboratory of Applied Microbiology South China, Guangdong Institute of Microbiology, Guangzhou 510070, China 2Department of Biology, Chengdu Normal University, Chengdu 611130, China

... introns of sequence analyses were predicted by web-based program FGENESH [37-39] (http://linux1.softberry.com/berry.phtml) Page 6. ... function proteins based on BLAST prediction and open reading frame (ORF) analysis by web-based SoftBerry (Supplementary files 2). ...


Gene
Volume 546, Issue 2, 10 August 2014, Pages 250–256 DOI: 10.1016/j.gene.2014.06.001

Nucleotide diversity of Pita, a major blast resistance gene and identification of its minimal promoter.

Ramkumar G. et al.,
a Biotechnology, Crop Improvement, DRR-ICAR, Hyderabad-30, India b Plant Pathology, DRR-ICAR, Hyderabad-30, India

... other default settings. Gene structure (length of open reading frame (ORF), number of exons/introns, etc.) and protein sequences were predicted using online tool softberry — FGENESH (http://linux1.softberry.com). Number of ...


Fungal biology
2014, 118(5), 453-461. DOI: 10.1016/j.funbio.2014.03.003

Molecular cloning and functional analysis of a H< sup>+-dependent phosphate transporter gene from the ectomycorrhizal fungus Boletus edulis in southwest China

Wang J. et al.,
Laboratory of Conservation and Utilization for Bioresources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming, Yunnan Province, PR China

... Bioinformatic analysis. The open reading frame (ORF) was predicted using the ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi) and the SoftBerry-FGENESH database (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...


Crop Science
2014, 54(3), 873-881. DOI: 10.2135/cropsci2013.09.0598

Fine Mapping of the Maize Cross-Incompatibility Locus Gametophytic Factor 1 (ga1) Using a Homogeneous Population.

Liu, X et al.,
2. Ajinomoto-Genetika Research Institute, 1st Dorozhny Pr. 1-1, 117545, Moscow, Russia 1. Syngas Biofuels Energy, Inc., P.O. Box 300819, Houston, TX, 77230, USA

... The maize gene set (www.maizesequence.org) and website-based software FGENSH (www.softberry.com) was applied to predict and filter the putative genes from the mapping interval. RESULTS. The Homogeneous Population Mapping Approach for Ga1-S Allele. ...


Applied microbiology and biotechnology
2014, 98(1), 285-296. DOI: 10.1007/s00253-013-5289-8

MpigE, a gene involved in pigment biosynthesis in Monascus ruber M7

Liu Q et al.,
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China 3. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China

... Amino acid sequence encoded by MpigE was predicted using SoftBerry's FGENESH program (http://linux1.softberry. com/berry.phtml), and the MpigE functional regions were analyzed using the Pfam 27.0 program (http://pfam.sanger.ac. uk/). ...


Gene
2014 DOI: 10.1016/j.gene.2014.01.008

The homoeologous genes encoding chalcone-flavanone isomerase in Triticum aestivum L.: structural characterization and expression in different parts of wheat plant

Shoeva, O. Y., Khlestkina, E. K., Berges, H., & Salina, E. A.
a Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia b Novosibirsk State University, 630090, Russia c INRA-CNRGV, Toulouse, 31326, France

... Gene annotation was performed by FGENESH program (Softberry Inc., linux1.softberry.com/berry.phtml) and confirmed by comparison of genomic nucleotide sequence with available ESTs. MEGA v5.1 software (Tamura et al. ...


Applied microbiology and biotechnology
2014,Volume 98, Issue 11, pp 4987-4994. DOI: 10.1007/s00253-014-5509-x

A promiscuous prenyltransferase from Aspergillus oryzae catalyses C-prenylations of hydroxynaphthalenes in the presence of different prenyl donors

Pockrandt, D., Sack, C., Kosiol, T., & Li, S. M.
1. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany

... Computer-assisted sequence analysis The software FGENESH (Softberry, Inc; http://www. softberry.com/berry.phtml) was used for prediction of exon and intron sequences. Alignments of amino acid sequences were carried out by using the program BLAST (http://blast. ...


Marine genomics
2014, 13, 1-9. DOI: 10.1016/j.margen.2013.10.004

Presence of two tumor necrosis factor ( tnf)-? homologs on different chromosomes of zebrafish ( Danio rerio) and medaka ( Oryzias latipes)

Kinoshita, S., Biswas, G., Kono, T., Hikima, J., Sakai, M.
a Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan b Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan c Interdisciplinary Research Organization, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan

... For medaka tnf-n, the nucleic acid sequence was retrieved from medaka chromosome 16 (25694643-25698981) (Ensembl release 72) and amino acid (aa) sequence, exons and introns were predicted using FGENESH in SoftBerry (http://linux1.softberry.com/berry.phtml). ...


Physiologia plantarum
, 150(1), 32-45. DOI: 10.1111/ppl.12064

Transcriptional regulation of the V?ATPase subunit c and V?PPase isoforms in Cucumis sativus under heavy metal stress

Kabala K. et al.,
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

... cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Journal of basic microbiology
28 APR 2014 DOI: 10.1002/jobm.201300814

Fan, L., Fu, K., Yu, C., Li, Y., Li, Y., & Chen, J. (2014). Thc6 protein, isolated from Trichoderma harzianum, can induce maize defense response against Curvularia lunata

Fan L. et al.,
Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China

... After predicting online on the softberry website (http://linux1.softberry.com/berry.phtml? topic=fgenesh&group=programs&subgroup=gfind) and using PCR for confirmation, we cloned a 710 bp cDNA fragment containing the T-DNA insertion site. ...


Plant Molecular Biology Reporter
2014, 1-21 DOI: 10.1007/s11105-014-0729-x

A Gene Encoding Cold-Circadian Rhythm-RNA Binding-Like Protein (CCR-Like) from Upland Cotton (Gossypium hirsutum L.) Confers Tolerance to Abiotic Stresses in Transgenic Tobacco

Dhandapani G. et al.,
1. National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India 2. Department of Plant Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

... The amplified cDNA was cloned in pGEM T-Easy vector and sequenced. The full- length cDNA sequence and coding sequence (CDS) were identified by the FGENESH analysis of softberry software (www.softberry.com/) and the sequence has been submitted to the GenBank. ...


Journal of experimental botany
2014, eru041. DOI: 10.1093/jxb/eru041

Sixteen cytosolic glutamine synthetase genes identified in the Brassica napus L. genome are differentially regulated depending on nitrogen regimes and leaf senescence.

Orsel M. et al.,
1 INRA, UMR 1349 Institut de Genetique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Universite de Rennes 1, F-35653 Le Rheu, France 2 INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49071 Beaucouze, France

...The deduced mRNA sequences (Supplementary Data File S5), obtained using FGENESH software available on the SoftBerry website (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group =programs&subgroup=gfind), showed very a high similarity with the contig sequences (Table 4) and allowed the gene structures to be deduced (Fig. 2). ...


Mycobiology
2014, 42(1), 34-40. DOI:10.5941/MYCO.2014.42.1.34

Three New Non-reducing Polyketide Synthase Genes from the Lichen-Forming Fungus Usnea longissima

Wang, Y., Wang, J., Cheong, Y. H., Hur, J. S.
1 Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming 650-204, China. 2 Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, Korea.

... Ltd. (Seoul, Korea). The potential open reading frame (ORF) was scanned with FGENESH [22] using Aspergillus as the matrix (http://linux1.softberry.com). The putative function of these ORFs was determined using a basic local alignment search tool (BLAST). ...


Molecular Breeding
2014, 33(4), 953-959. DOI:10.1007/s11032-013-0009-8

Intron loss in the chalcone-flavanone isomerase gene of rye

Khlestkina E. K., Shoeva O. Y.
1. Institute of Cytology and Genetics SB RAS, Lavrentjeva Ave. 10, 630090, Novosibirsk, Russia 2. Novosibirsk State University, Novosibirsk, Russia

... Gene structure was determined by FGENESH software (http://?linux1.?softberry.?com/?berry.? phtml, Solovyev 2007 ) and confirmed by comparison of nucleotide sequence with the rye expressed sequence tag BE705313 (http://?www.?ncbi.?nlm.?nih.?gov/?Database/?). ...


Food chemistry
2014, 148, 381-387 DOI: 10.1016/j.foodchem.2013.10.062

Two xylose-tolerant GH43 bifunctional ?-xylosidase/?-arabinosidases and one GH11 xylanase from Humicola insolens and their synergy in the degradation of xylan

Yang X. et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China b Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China

... deduce the amino acid sequences, respectively. The online software FGENESH (http://linux1.softberry.com/berry.phtml) was used to predict the transcription initiation sites, introns and exons. SignalP4.0 server (http://www.cbs ...


Acta Biochimica Polonica
2014, 61(1), 19-22. on-line at: www.actabp.p

Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker

Macko-Podgorni A. et al.,
1 Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Krakow, Poland; 2 Department of Horticulture, University of Wisconsin-Madison, Madison, USA; 3 USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, USA

... reported by Iorizzo et al. (2012) with blastn on a local BLAST server. The identified con- tig was searched for presence of coding regions using FGENESH (http://linux1.softberry.com/berry.phtml). The sequence was searched for ...


Molecular biology reports
July 2014, Volume 41, Issue 7, pp 4305-4312 DOI:10.1007/s11033-014-3301-8

RNAi Mediated curcin precursor gene silencing in Jatropha (Jatropha curcas L.)

Patade V. Y. et al.,
1. Defence Institute of Bio-Energy Research, Haldwani-263 139, Nainital, Uttarakhand, India

... commercially (Eurofins, India). The sequence was analyzed for homology using Blast program [ 22 ]. The gene structure was predicted using FGENESH 2.6 tool (http://?linux1.?softberry.?com/?berry.?phtml). The Motif scanning ...


Nature
2014, 511(7508), E7-E9. DOI:10.1038/nature13446

TH2 and Treg candidate genes in elephant shark

Dijkstra, J. M.
Institute for Comprehensive Medical Science, Fujita Health University, Dengaku-gakubo 1-98, 470-1192 Toyoake, Aichi, Japan

... 2, the loop between ?-helices A and B; exon 3, ?-helices B and C; exon 4, ?-helix D. Genes without messenger RNA reports were predicted from genomic DNA sequences using GENSCAN (http://genes.mit.edu/GENSCAN.html) or FGENESH (http://linux1.softberry.com/berry ...


Plant Breeding
Volume 133, Issue 4, pages 470–479, August 2014 DOI:10.1111/pbr.12190

Genetic and functional analysis of tocopherol biosynthesis pathway genes from rapeseed (Brassica napus L.)

Fritsche S. et al.,
1 Plant Breeding Institute, Christian-Albrechts University of Kiel, Kiel, Germany 2 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

... Institute 2012). Sequence comparisons were performed with the basic local alignment search tool (BLAST). Intron–exon structures were predicted with the bioinformatic tool FGENESH (SoftBerry FGENESH 2007). The NCBI ...


Plant molecular biology
2014, 84(1-2), 95-110 DOI:10.1007/s11103-013-0121-5

Association of jacalin-related lectins with wheat responses to stresses revealed by transcriptional profiling

Song M. et al.,
1. Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People’s Republic of China 2. Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, 270-0061, Baiyun Road, Guiyang, 550008, People’s Republic of China

... overlapped regions. Gene prediction was then performed using the gene-finding program FGENESH (http://?www.?softberry.?com/?), and the coding DNA sequences were verified by alignment with the homologous ESTs. Domain ...


DNA Research
2014, dsu016 DOI:10.1093/dnares/dsu016

Evolutionary History of Trihelix Family and Their Functional Diversification

Qin Y. et al.,
1 State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China 2 Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea

... a cut-off value of e ?10 . As for confirmation of the predicted genes, manual correction was performed using the online web server FGENESH (http://linux1.softberry.com/ berry.phtml). 28 The confirmed sequences were further ...


Gene
2014, 544(1), 83-92 DOI:10.1016/j.gene.2014.04.046

Genome-wide analysis of terpene synthases in soybean: functional characterization of GmTPS3

Liu J. et al.,
a National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China b Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China

... soybean genome sequence assembly using TBLASTN. The gene prediction program FGENESH (http://www.softberry.com) was used to predict the open reading frames of putative TPS genes. Protein sequences deduced from the ...


Frontiers in Plant Science | Plant Genetics and Genomics
2014, 5, 339. DOI:10.3389/fpls.2014.00339

Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris)

Jackson, S.
1 Center forAppliedGeneticTechnologies,UniversityofGeorgia,Athens,GA,USA 2 US DepartmentofEnergyJointGenomeInstitute,WalnutCreek,CA,USA

... carry an extra ORF coding envelope-like proteins, the internal regions of 65 Ty1-copia and 78 Ty3-gypsy families were annotated using FGENESH (http://linux1.softberry.com) and ... (http://linux1.softberry.com) and GENSCAN (http://genes.mit.edu/GENSCAN.html) programs. ...


Plant Molecular Biology Reporter
2014, 32(2), 476-486. DOI: 10.1007/s11105-013-0666-0

Molecular Cloning and Characterization of a Novel Polygalacturonase Gene, BcMF24, Involved in Pollen Development of Brassica campestris ssp. chinensis

Yu Y. et al.,
1. Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China

... Full CDS sequences were analyzed by FGENESH (http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&subgroup=gfind), and the molecular characteristic of the deduced protein was viewed on the ExPASy (http://web.expasy.org/compute_pi/). ...


Middle-East Journal of Scientific Research
2014, 20(3), 391-395. DOI:10.5829/idosi.mejsr.2014.20.03.11465

An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Genomic Library for Osmium baselicum Plant.

Shah, G. C., Gupta, V., Khanuja, S. P. S.
1 Rajiv Gandhi College Satna M.P. India 2 Entral Institute of Medicinal and Aromatic Plant Lucknow U.P. India

... a new family, the oxidatively stable proteases previously p a r a m e t e r s thought to be present only in bacteria. Phylogenetic http:linux1.softberry.coberry.phtml?topic=fgenesh&grp= studies showed that many gene duplications and loss ograms&sub group=gfind. ...


Applied microbiology and biotechnology
2014, 98(11), 5019-5028. DOI:10.1007/s00253-014-5533-x

A novel bifunctional pectinase from Penicillium oxalicum SX6 with separate pectin methylesterase and polygalacturonase catalytic domains

Tu T. et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China

... as Lu and Moriyama (2004) described. Transcription initiation sites, intron, and exon were predicted using the online software FGENESH (http://linux1.softberry. com/berry.phtml/). Nucleotide and deduced amino acid sequence ...


Journal of industrial microbiology & biotechnology
2014, 41 (7), 1071-1083. DOI:10.1007/s10295-014-1453-0

A new acidophilic endo-b-1, 4-xylanase from Penicillium oxalicum: cloning, purification, and insights into the influence of metal ions on xylanase activity

Liao H. et al.,
1. Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China 2. Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China

... Putative signal peptides were predicted using signalP (http://www.cbs.dtu.dk/services/ signalP/). The exon–intron structure of the full-length gene was predicted using the online software fgenesh (http://linux1.softberry.com/ berry.phtml). ...


Crop and Pasture Science
2014, 65(1), 38-45. DOI:10.1071/CP13140

Isolation and characterisation of cytosolic glutamine synthetase (GSe) genes and association with grain protein content in durum wheat

Gadaleta, A. et al.,
A Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A – 70126 Bari, Italy.

... Genes prediction was conducted with the FGENESH program (http://linux1.softberry.com/berry. phtml?topic=fgenes handgroup=programsandsubgroup=gfind). Consensus exon/ introns boundaries were confirmed using grass expressed sequence tag sequences aligned to the ...


ChemBioChem
2014, 15(1), 108-116. DOI:10.1002/cbic.201300610

AstPT Catalyses both Reverse N1?and Regular C2 Prenylation of a Methylated Bisindolyl Benzoquinone

Tarcz S. et al.,
Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, 35037 Marburg (Germany)

... Computer-assisted sequence analysis: The software packages DNASIS (version 2.1; Hitachi Software Engineering, San Bruno, CA, USA) and FGENESH (Softberry, Inc; http://www.softberry. com/berry.phtml) were used for intron prediction and sequence analysis, respectively. ...


Molecular biology reports
2014, 1-12. DOI:10.1007/s11033-014-3360-x

GhPSY, a phytoene synthase gene, is related to the red plant phenotype in upland cotton (Gossypium hirsutum L.)

Cai C. et al.,
1. State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

... Gene prediction was performed using the Fgenesh program in MolQuest software v1.3.1 (http://?linux1.?softberry.?com/?berry.?phtml), and predicted genes and their GO (Gene Ontology) categories were annotated with the Blast2GO program ([ 18 ], http://?www.?blast2go ...


PloS one
2014, 9(1), e87723. DOI:10.1371/journal.pone.0087723

Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome

Wang, J. et al.,
Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China, School of Science, Huazhong Agricultural University, Wuhan, P.R. China

... 8, detailed information includes the final gene model, RNA-seq and RNA-PET data from different tissues, ESTs from sweet orange and other citrus species, and four ab initio gene prediction tools, ie, Genscan [17], GeneID [18], FgeneSH (http://linux1.softberry.com/berry.phtml ...


Genome biology and evolution
2014, evu112 DOI: 10.1093/gbe/evu112

Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals

Zhang, H. H., Feschotte, C., Han, M. J., Zhang, Z.
1School of Life Sciences, Chongqing University, Chongqing 400044, China 2 College of Life Sciences, Jiujiang University, Jiujiang 332000, China

... Sequence analysis Potential open reading frame (ORF) of Chapaev elements used in this study was predicted using FGENESH (http://linux1.softberry.com/berry.phtml), GENSCAN (http://genes.mit.edu/GENSCAN.html) or getorf in EMBOSS-6.3.1 package (Rice et al. 2000) ...


Molecular Genetics and Genomics
April 2014. DOI:10.1007/s00438-014-0848-y

High-resolution genetic mapping of rice bacterial blight resistance gene Xa23

Wang C. et al.,
1. National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, People’s Republic of China 2. Liaocheng University, Liaocheng, 252059, Shandong Province, People’s Republic of China

... Based on the targeted region of Xa23 locus, genomic sequence of nipponbare between the markers lj138 and a83B4 was downloaded from nCBI (http://www.ncb i.nlm.nih.gov) and analyzed using the online software FGeneSH (http://linux1.softberry.com/). ...


FGENESH 2013

Applied Microbiology and Biotechnology
October 2013 DOI: 10.1007/s00253-013-5289-8

MpigE, a gene involved in pigment biosynthesis in Monascus ruber M7

Liu, et al.,
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China 3. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People’s Republic of China

... Amino acid sequence encoded by MpigE was predicted using SoftBerry's FGENESH program (http://linux1.softberry. com/berry.phtml), and the MpigE functional regions were analyzed using the Pfam 27.0 program (http://pfam.sanger.ac. uk/). ...


New Phytologist
200: 820–833. doi: 10.1111/nph.12396

Plant Defensin type 1 (PDF1): protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri.

Shahzad et al.,
1Biochimie et Physiologie Moleculaire des Plantes, Unite Mixte de Recherche Montpellier, SupAgro/CNRS/INRA/Universite Montpellier II, Montpellier Cedex 1, France 2Montpellier SupAgro, UMR AGAP, Montpellier, France

... Genes were predicted using the FGENESH program (Salamov & Solovyev, 2000) under the SOFTBERRY software (www.softberry.com) and were annotated based on BLAST similarity searches (Altschul et al., 1990). The presence ...


Cell Stress and Chaperones
Volume 18, Issue 3 , pp 321-331 DOI:10.1007/s12192-012-0384-9

Functional relevance of J-protein family of rice (Oryza sativa)

Neelam K Sarkar, Upasna Thapar, Preeti Kundnani, Priyankar Panwar, Anil Grover
1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India

... FGENESH analysis of genomic sequence of Os03g12236 at softberry (www.softberry. com/) revealed presence of one gene having 10 exons coding for 462 amino acid protein. The amino acid sequence deduced from softberry ...


Phytopathology
November 2013, Volume 103, Number 11 Pages 1162-1168 http://dx.doi.org/10.1094/PHYTO-02-13-0044-R

Fine Mapping and Identification of Blast Resistance Gene Pi-hk1 in a Broad-Spectrum Resistant japonica Rice Landrace

Wu et al.,
State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. Y. Wu and Y. Bao contributed equally to this work.

... (http://genes.mit.edu/GENSCAN.html) and softberry (http://linux1.softberry.com/berry.phtml). The predicted introns about 200-500bp were ... Page 7 of 28 Page 8. 8 FGENESH (http://linux1. softberry.com/) and RiceGAAS (http://rgp.dna.affrc.go.jp) software (32). ...


Biotechnology Letters
Volume 35, Issue 9 , pp 1425-1432 DOI:10.1007/s10529-013-1219-1

Deletion of pigR gene in Monascus ruber leads to loss of pigment production

Nana Xie, Qingpei Liu, Fusheng Chen
1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China 2. State Key Laboratory of Agricultural Microbiology, Wuhan, 430070, Hubei, China

... agitation. Three replicates of each sample were carried out. Sequence analysis. Amino acid sequence encoded by pigR was predicted using the SoftBerry's FGENESH program (http://linux1.softberry.com/berry.phtml). Homology ...


Heredity
(2013) 111, 57–65; doi:10.1038/hdy.2013.19; published online 3 April 2013

The discovery of Foxl2 paralogs in chondrichthyan, coelacanth and tetrapod genomes reveals an ancient duplication in vertebrates

M T Geraldo 1, G T Valente 1, A SK Braz 2 and C Martins 1
1Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, Sao Paulo State University–UNESP, Botucatu, Sao Paulo, Brazil 2Laboratory of Computational Biology and Bioinformatics, Center of Natural and Human Sciences, Federal University of ABC–UFABC, Santo Andre, Sao Paulo, Brazil

... The sequences acquired were inserted into the online program Softberry FGENESH (http://www.softberry.com/) using T. rubripes as the reference genome to recover the whole gene transcriptional region and confirm the identification of genes in these syntenic regions ...


Microbiological Research
Volume 168, Issue 6, 19 July 2013, Pages 340–350 DOI: 10.1016/j.micres.2013.01.005

Identifying pathogenicity genes in the rubber tree anthracnose fungus Colletotrichum gloeosporioides through random insertional mutagenesis

Cai et al.,
a Environment and Plant Protection College, Hainan University, Danzhou, Hainan 571737, China b Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan 571737, China

... Sixteen T-DNA integration sites of transformants impaired in pathogenicity were identified, and in most cases T-DNA integrated into a predicted ORF of putative genes based on gene structure prediction by FGENESH program (Softberry Inc., Mount Kisco, NY, USA, http://linux1 ...


Cell Biology International
(2013) 37: 687–693. doi: 10.1002/cbin.10080

Computational prediction and characterisation of ubiquitously expressed new splice variant of Prkaca gene in mouse.

Banday, A. R., Azim, S., Hussain, M. A., Nehar, S. and Tabish, M.
1Faculty of Life Sciences, Department of Biochemistry, A.M. University, Aligarh, Uttar Pradesh, India 2P.G. Department of Zoology, Ranchi University, Ranchi, Jharkhand, India

.. were used at HMM gene (http://www.cbs.dtu.dk/services/HMMgene) (Lukashin and Borodovsky, 1998), Genescan (http://genes.mit.edu/GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/ software/GeneSplicer/) (Pertea et al., 2001), FGENESH (http://www.softberry.com/berry ...


Nucl. Acids Res.
(1 January 2013) 41 (D1): D1192-D1198. doi: 10.1093/nar/gks1090

OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants

Pan et al.,
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, 2Shanghai Center for Bioinformation Technology, Shanghai 200235 and 3Tarim University, Alar, Xinjiang 843300, China

... Constructing the starting dataset of small peptides (25–250 aa in length) by combining data from whole-genome screening and from gene modeling using Augustus (v2.5.5) and FGENESH (Softberry, http://www.softberry.com) (34). ...


Trends in Bioinformatics
2013, Vol. 6 Issue 3, p62-90. 29p.

In-silico Study of Transcription Factor Binding Elements of Human PAX Gene Family Members

Rashmi et al.,

... For study of cis-acting elements-4000 upstream regions were retrieved using NCBI. Cis-acting elements analysis were done using fgenesh tool of softberry server (http://linuX1 .softberry.com/berry.phtml; Solovyev and Salamov, 1997). ...


Genes & Genomics
Volume 35, Issue 2 , pp 159-166 DOI:10.1007/s13258-013-0075-7

Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity

Jungmin Ha, Puji Lestari, Suk-Ha Lee
1. Department of Plant Science and Research Institute for Agriculture and Life Science, Seoul National University, Seoul, 151-921, Korea 2. Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar No. 3A, Bogor, 16111, Indonesia

... BLAST algorithm. Any putative genes were also investigated with the FGENESH software (http://linux1.softberry.com/berry.phtml) using the dicot plant option (Arabidopsis). Primer design and PCR amplification. To amplify the ...


Physiologia Plantarum
Volume 150, Issue 1, pages 32–45, January 2014 DOI:10.1111/ppl.12064

Transcriptional regulation of the V-ATPase subunit c and V-PPase isoforms in Cucumis sativus under heavy metal stress

Katarzyna Kabala*, Malgorzata Janicka-Russak, Malgorzata Reda, Magdalena Migocka
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

.. cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Russian Journal of Plant Physiology
Volume 60, Issue 5 , pp 713-719 DOI:10.1134/S102144371305004X

Cloning and characterization of ethylene-insensitive 2 (EIN2) gene from Cucumis melo

F. Gao, J. Hao, Y. Yao, X. Wang, A. Hasi
1. College of Life Sciences, Inner Mongolia University, Hohhot, 010021, P.R. China 2. Inner Mongolia Key Laboratory of Herbage and Endemic Crop Biotechnology, Hohhot, 010021, P.R. China

... tigs that contain the genomic DNA sequence of the putative CsEIN2. (3) The gene prediction program Softberry of FGENESH (http://linux1.soft berry.com/berry.phtml) was used to predict multiple (alternative splice) variants of potential CsEIN2 genes in the cucumber genome ...


European Journal of Plant Pathology
Volume 137, Issue 1 , pp 55-65 DOI:10.1007/s10658-013-0216-5

Mining of rice blast resistance gene Pi54 shows effect of single nucleotide polymorphisms on phenotypic expression of the alleles

Kumari et al.,
1. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Room No 39, LBS Centre, Pusa Campus, New Delhi, 110012, India 2. Division of Crop Improvement, Indian Institute of Pulses Research, Kanpur, 208 024, Uttar Pradesh, India

... Eur J Plant Pathol Page 3. using Primer 3 software (www.softberry.com). The ... Eur J Plant Pathol Page 4. performed to predict gene structure and ORF region using FGENESH software trained for monocot (www.softberry.com). The ...


Phil. Trans. R. Soc. B
19 September 2013 vol. 368 no. 1626 20130047 DOI:10.1098/rstb.2013.0047

Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses

Bezier et al.,
1Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Universite Francois Rabelais, Parc de Grandmont, 37200 Tours, France 2Commissariat a l'Energie Atomique, Genoscope (Centre National de Sequencage), 2 rue Gaston Cremieux, CP 5706, 91057 Evry Cedex, France

... For both Cotesia spp., gene predictions were performed using a combination of FGENESH and FGENESH+ software from the SoftBerry platform with the Apis mellifera training set (http://linux1.softberry.com/all.htm) and from the EMBL-EBI platform using Wise2 algorithms (http ...


Theoretical and Applied Genetics
Volume 126, Issue 1 , pp 219-229 DOI:10.1007/s00122-012-1975-7

Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.)

Huang et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Agricultural College, Guangxi University, Nanning, 530005, China 2. Rice Research Institute, Plant Protection Institute and Guangxi Rice Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China

... The putative open reading frame (ORF) in the target region was predicted by the online software GENESCAN and FGENESH of Softberry (www.softberry.com/berry.phtml) with monocot plants as the model organism. Host selection behavior ...


Microbiology
October 2013 vol. 159 no. Pt 10 2169-2179 DOI:10.1099/mic.0.069542-0

CdpC2PT, a reverse prenyltransferase from Neosartorya fischeri with a distinct substrate preference from known C2-prenyltransferases

Kathrin Mundt 1,2 and Shu-Ming Li 1,2
1Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037 Marburg, Germany 2Zentrum fur Synthetische Mikrobiologie, Philipps-Universitat Marburg, 35032 Marburg, Germany

... al., 1988). Computer-assisted sequence analysis. For intron prediction and sequence analysis, fgenesh (http://linux1.softberry.com) and dnasis (v. 2.1; Hitachi Software Engineering) were used, respectively. Sequence identities ...


Molecular Genetics and Genomics
Volume 288, Issue 3-4 , pp 111-129 DOI:10.1007/s00438-013-0733-0

Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato

Zejun Huang, Jason Van Houten, Geoffrey Gonzalez, Han Xiao, Esther van der Knaap
1. Department of Horticulture and Crop Science, The Ohio State University/OARDC, 217A Williams Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA

... solgenomics.net). We identified nine genes that were not in database ITAG Release 2.3 but appear to have protein coding potential based on annotation by FGENESH (http://linux1.softberry.com/berry.phtml). Initial evidence ...


Euphytica
December 2013 DOI:10.1007/s10681-013-1037-5

Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)

Yang et al.,
1. School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Minhang District, Shanghai, 200240, China 2. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, 201602, China

... (Voorrips 2002 ). Gene prediction in the target genomic DNA regions was performed using the program FGENESH (Salamov and Solovyev 2000 ) (http://linux1.softberry. com/), and the results were checked manually. Results. ...


Plant and Soil
Volume 364, Issue 1-2 , pp 245-260 DOI:10.1007/s11104-012-1345-x

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

M. Migocka, A. Warzybok, G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland

... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was determined using FGENESH or FGENESH+ programs available on softberry.com ...


Tree Genetics & Genomes
November 2013 DOI:10.1007/s11295-013-0678-9

Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance

Schouten et al.,
1. Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands 2. Inova Fruit, P.O. Box 222, 4190 CE, Geldermalsen, The Netherlands 3. Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitatstrasse 2, 8092, Zurich, Switzerland

... 2010b) was copied from the NCBI database (accession number GU295057.1). The Vr2-A, Vr2-B, and Vr2-C amino acid sequences in GMAL 2473 were predicted by means of the publicly available software FGENESH from SoftBerry. ...


Applied Biochemistry and Biotechnology
Volume 169, Issue 3 , pp 941-949 DOI:10.1007/s12010-012-0048-3

Molecular Cloning and Expression of a Novel b-Glucosidase Gene from Phialophora sp. G5

Xuejun Li et al.,
1. Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China 2. Beijing Challenge Bio-Technology Co., Ltd., Beijing, 100081, People’s Republic of China

... designed on the assembled sequence. Sequence Analysis The introns, exons, and transcription initiation sites were analyzed by FGENESH (http:// www.softberry.com/ berry.phtml/). Amino acid and nucleotide sequence alignments ...


Immunogenetics
Volume 65, Issue 7 , pp 531-541 DOI:10.1007/s00251-013-0692-y

IgH loci of American alligator and saltwater crocodile shed light on IgA evolution

Susana Magadan-Mompo, Christian Sanchez-Espinel, Francisco Gambon-Deza
1. Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo, 36210, Pontevedra, Spain 3. Oceanographic Center of Vigo, Spanish Institute of Oceanography (IEO), Subida a Radio Faro 50, 36390, Vigo, Pontevedra, Spain

... Exons coding for the CH immunoglobulin domains were identified by aligning genomic and predicted amino acid sequences with previously published reptile immunoglobu- lin sequences. Limits were deduced using the FGENESH (www.softberry.com) (Solovyev et al. ...


Applied Microbiology and Biotechnology
Volume 97, Issue 4 , pp 1649-1660 DOI:10.1007/s00253-012-4130-0

Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides

Suqin Yin, Xia Yu, Qing Wang, Xiao-Qing Liu, Shu-Ming Li
1. College of Life Sciences, Capital Normal University, No.105 Xisanhuan Beilu, Beijing, 100048, China 2. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany

... Computer-assisted sequence analysis FGENESH (Softberry, Inc.) and the DNASIS software pack- age (version 2.1: Hitachi Software Engineering, San Bruno, CA) were used for intron prediction and sequence analysis, respectively. ...


PloS one
July 09, 2013DOI: 10.1371/journal.pone.0068260

A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes

Kenji K. Kojima, Jerzy Jurka
Genetic Information Research Institute, Mountain View, California, United States of America

... copies. Exon-intron boundaries were predicted with the aid of SoftBerry FGENESH: (http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup= gf?ind) and GENEID (http://genome.crg.es/geneid.html). ...


International Journal of Genomics and Proteomics
Volume 4, Issue 1, 2013, pp.-64-71 Available online at http://www.bioinfopublication.org/jouarchive.php?opt=&jouid=BPJ0000227

MOLECULAR MODELING OF ?-AMYLASE FROM GERMINATED SOYBEAN (Glycine max) AND ITS FUNCTIONAL DIVERSITY

KUMARI A. 1, SINGH V.K. 2 AND KAYASTHA A.M. 1
1School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221 005, UP, India. 2Centre for Bioinformatics, School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221 005, UP, India.

... It showed similarity with Glycine max strain Wil- liams 82 clone GM_WBb0115J10 (AC235387.1). Full length gene prediction was done for obtained strain using Fgenesh (http:// sun1.softberry.com/berry.phtml) and -1000 upstream region was retrieved for promoter study ...


Food Chemistry
Volume 141, Issue 3, 1 December 2013, Pages 2974–2981 DOI:10.1016/j.foodchem.2013.05.132

High-yield production of a low-temperature-active polygalacturonase for papaya juice clarification

Tao Tu et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China b Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China

... Multiple alignments of protein sequences were performed using the ClustalW program (http://www.ebi.ac.uk/clustalW/). Transcription initiation sites, intron, and exon were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml/). ...


Immunogenetics
Volume 65, Issue 5 , pp 387-396 DOI:10.1007/s00251-013-0678-9

Immunoglobulin light chains in medaka (Oryzias latipes)

Susana Magadan-Mompo, Anastasia M. Zimmerman, Christian Sanchez-Espinel, Francisco Gambon-Deza
1. Virologie et Immunologie Moleculaires, Institut National de la Recherche Agronomique (INRA), Domaine de Vilvert, 78352, Jouy-en-Josas, France 2. Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA

... 2009; Zimmerman et al. 2008; Bao et al. 2010). Boundaries of exons were deduced using the software packages FGENESH (www.softberry.com) (Solovyev et al. 2006) and Augustus (http://augustus.gobics.de/submission) (Stanke et al. ...


Mol Biol Rep.
2013 Mar;40(3):2645-62. doi: 10.1007/s11033-012-2351-z. Epub 2012 Dec 15.

Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa).

Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa). et al.,
CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.

... Local blast was performed using Arabid- opsis CDPK and its closely related kinase proteins as queries for the identification of genes from Populus. Manual reanno- tation was also performed using online web server FGENESH (http://linux1.softberry.com/berry.phtml). ...


Process Biochemistry
Volume 48, Issue 12, December 2013, Pages 1879–1885 DOI:10.1016/j.procbio.2013.08.020

A novel thermophilic xylanase from Achaetomium sp. Xz-8 with high catalytic efficiency and application potentials in the brewing and other industries

Zhao et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China b College of Life Science, Capital Normal University, Beijing 100048, PR China

... Genes, introns, exons and transcription initiation site were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted using SignalP 4.1 Server (http://www.cbs.dtu.dk/services/SignalP/). ...


Plant Molecular Biology Reporter
October 2013 DOI:10.1007/s11105-013-0666-0

Molecular Cloning and Characterization of a Novel Polygalacturonase Gene, BcMF24, Involved in Pollen Development of Brassica campestris ssp. chinensis

Youjian Yu, Meiling Lv, Ying Liang, Xingpeng Xiong, Jiashu Cao
1. Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China

... Full CDS sequences were analyzed by FGENESH (http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&subgroup=gfind), and the molecular characteristic of the deduced protein was viewed on the ExPASy (http://web.expasy.org/compute_pi/). ...


J. Agric. Food Chem.,
2013, 61 (28), pp 6880–6889DOI: 10.1021/jf4001296

Two Family 11 Xylanases from Achaetomium sp. Xz-8 with High Catalytic Efficiency and Application Potentials in the Brewing Industry

Zhao et al.,
† Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China ‡ College of Life Science, Capital Normal University, Beijing 100048, People’s Republic of China

... Genes, introns, exons, and transcription initiation sites were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted using SignalP 4.0 Server (http://www.cbs.dtu.dk/services/SignalP/). ...


Applied Microbiology and Biotechnology
Volume 97, Issue 18 , pp 8121-8128 DOI:10.1007/s00253-012-4656-1

A family 5 b-mannanase from the thermophilic fungus Thielavia arenaria XZ7 with typical thermophilic enzyme features

Lu et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China 2. College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 3000457, People’s Republic of China

... nih.gov/gorf/gorf/gorf.html). The sequence assembly was per- formed using the Vector NTI Advance 10.0 software (Invitrogen). Genes, introns, exons, and transcription initia- tion sites were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...


Mycorrhiza
Volume 23, Issue 7 , pp 573-584 DOI:10.1007/s00572-013-0498-7

The reduced mycorrhizal colonisation (rmc) mutation of tomato disrupts five gene sequences including the CYCLOPS/IPD3 homologue

Larkan et al.,
1. School of Plant Biology M090, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia, 6009, Australia 2. Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N0X2, Canada 3. Donald Danforth Plant Science Centre, 975 N Warson Rd, St Louis, MO, 63132, USA

... Page 6. Genes within this sequence were predicted using FGENESH software (softberry.com). ... FGENESH gene prediction software (softberry.com) was used to annotate the region and to determine whether any match to known mycorrhiza-regulating genes could be identified. ...


Eukaryotic Cell
September 2013 vol. 12 no. 9 1214-1224 DOI:10.1128/EC.00159-13

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

Yang et al.,
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USAa Department of Microbiology, University of Hong Kong, Hong Kongb Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China

... Genes with a false discovery rate (FDR) of <0.05 as reported by all three packages were considered to be differentially expressed. Gene prediction and identification of orthologs.Ab initio gene predictions were performed using FGENESH (SoftBerry, Mount Kisco, NY). ...


Crop and Pasture Science
DOI:10.1071/CP13140

Isolation and characterisation of cytosolic glutamine synthetase (GSe) genes and association with grain protein content in durum wheat

Gadaleta et al.,
A Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A – 70126 Bari, Italy.

... Genes prediction was conducted with the FGENESH program (http://linux1.softberry.com/berry. phtml?topic=fgenes handgroup=programsandsubgroup=gfind). Consensus exon/ introns boundaries were confirmed using grass expressed sequence tag sequences aligned to the ...


Appl. Environ. Microbiol.
March 2013 vol. 79 no. 6 2038-2047 DOI:10.1128/AEM.03334-12

Characterization of the Biosynthetic Genes for 10,11-Dehydrocurvularin, a Heat Shock Response-Modulating Anticancer Fungal Polyketide from Aspergillus terreus

Xu et al.,
aNatural Products Center, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, Tucson, Arizona, USA bInstitut fur Chemie, Technische Universitat Berlin, Berlin, Germany

... earlier (17). Hidden Markov model (HMM)-based gene models were built with FGENESH (Softberry) with additional exon/intron boundary refinements in SPLICEVIEW (http://zeus2.itb.cnr.it/?webgene/wwwspliceview.html). The ...


IJEB
Vol.51(12) [December 2013] pp. 1130-1136

Molecular cloning and mRNA expression profile of Sucrose Transporter Gene BnSUT1C from Brassica napus L.

Li et al.,

... suite (Windows version 5.0.2; DNASTAR, Madison, Wis.). The complete open reading frame (ORF) was identified with program FGENESH (http://www.softberry.com/berry. phtml). Primers were designed in the predicted 5' and ...


Advanced BioTech
Volume:12 Issue:11 May 10, 2013

Isolation and in silico Depiction of Novel R2-R3 MYB Transcription Factors from Sugarcane

Pranali A. Kulkarni1, Prabu G.R. and Rachayya M. Devarumath
1. Molecular Biology & Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk.), Tal. Haveli, Pune-412307, Maharashtra, India. 2. Department of Biotechnology, University of Pune, Pune-411005, Maharashtra, India. 3. Department of Biotechnology, School of Life Sciences, Karpagam University, Pollachi Coimbatore – 641021, Tamil Nadu, India.

... The nucleotide sequences of SbMYB18 and SoMYB18 were processed for deducing the exon and intron pattern online using fGENESH Hidden Markov Model (HMM) based gene structure prediction tool (www.softberry.com/berry.phtml). ...


Plant Molecular Biology Reporter
Volume 31, Issue 6 , pp 1249-1260 DOI:10.1007/s11105-013-0585-0

Structure, Evolution, and Expression of the b-Galactosidase Gene Family in Brassica campestris ssp. chinensis

Jinlong Liu, Minghui Gao, Meiling Lv, Jiashu Cao
1. Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China

... Each of the BGAL gene loci in Arabidopsis was used to obtain all possible BGAL genes in B. campestris from BRAD (Table 1). Each predicted BGAL gene sequence in B. campestris was confirmed by FGENESH (http://www.softberry.com/berry.phtml?topic=fgenesh). ...


PloS one
May 28, 2013DOI: 10.1371/journal.pone.0064432

Adaptive Selection on Bracovirus Genomes Drives the Specialization of Cotesia Parasitoid Wasps

Jancek et al.,
Institut de Recherches sur la Biologie de l’Insecte, UMR 7261 CNRS, Universite Francois-Rabelais, UFR Sciences et Techniques, Parc Grandmont, Tours, France aboratoire Evolution, Genomes et Speciation, CNRS UPR9034, IRD UR 072 and Universite Paris Sud, Gif sur Yvette, France, Unite de Recherche UMR 1272, Physiologie de l’Insecte, Signalisation et Communication, INRA, Versailles, France

... Gene predictions on CskBV newly sequenced contigs and BACs and on CsmBV BACs were made with SoftBerry's FGENESH de novo prediction tool [37] and FGENESH+ using the honeybee (Apis mellifera L.) training set and were manually corrected by comparison with ...


Molecular Immunology
Volume 56, Issue 4, 31 December 2013, Pages 745–756 DOI:10.1016/j.molimm.2013.07.012

Accessory molecules for Toll-like receptors in Teleost fish. Identification of TLR4 interactor with leucine-rich repeats (TRIL)

Danilo Pietretti a, Herman P. Spaink b, Alberto Falco a, Maria Forlenza a, Geert F. Wiegertjes a,
a Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands b Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands

... al., 2012). Genomic information was then used to predict nucleotide and protein sequences using FGENESH version 2.5 (www.softberry.com). Table 1. Accessory molecules present in teleost fish species. Accessory molecules ...


Theoretical and Applied Genetics
October 2013 DOI:10.1007/s00122-013-2205-7

A putative candidate for the recessive gall midge resistance gene gm3 in rice identified and validated

Sama et al.,
1. Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, Andhra Pradesh, India 2. International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Andhra Pradesh, India

... The down- loaded sequences were then analyzed using the software package FGeneSH (http://www.softberry.com) for open reading frames (OrFs) and annotated using BlAST-P utility (http://www.ncbi.nlm.nih.gov) to identify the puta- tive function of each gene present in the ...


Plant Cell Reports
November 2013, DOI:10.1007/s00299-013-1535-x

Transcriptional regulation of early embryo development in the model legume Medicago truncatula

Sergey Kurdyukov, Youhong Song, Michael B. Sheahan, Ray J. Rose
1. Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia 2. Kolling Institute of Medical Research, Kolling Building, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia

... The corresponding gene loci and protein sequences were obtained from the Mt3.5 genome release (http://www.medicagohapmap.org), or where unavailable, they were predicted directly using FGENESH (http://www.softberry.com). ...


J Hered
(2013) 104 (1): 134-139. doi: 10.1093/jhered/ess075

Localization of a New Gene for Bitterness in Cucumber

Zhang et al.,
From the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081 China (Zhang, Miao, Sun, Wang, Huang, and Gu); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).

... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and verified by FGENESH (http://sunl.softberry.com/) (Salamov and Solovyev 2000), GENESCAN (http://genes.mit.edu/GENSCAN.html) (Burge and Karlin 1997), TwinScan (http://mblab ...


Arthropod-Plant Interactions
Volume 7, Issue 4 , pp 389-402 DOI:10.1007/s11829-013-9253-4

Hessian fly larval attack triggers elevated expression of disease resistance dirigent-like protein-encoding gene, HfrDrd, in resistant wheat

Subhashree Subramanyam, Cheng Zheng, John T. Shukle, Christie E. Williams
1. Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA 2. Novartis Pharmaceuticals Corporation, East Hanover, NJ, 07936, USA

... subcellular localization of HFRDRD proteins. Structural analysis of the genomic sequence was performed using the FGENESH program (http://linux1.softberry.com/berry.phtml). Phylogenetic analysis. In order to explore the evolutionary ...


Microbial Pathogenesis
Volume 64, November 2013, Pages 6–17 DOI:10.1016/j.micpath.2013.06.001

Identification of virulence genes in the crucifer anthracnose fungus Colletotrichum higginsianum by insertional mutagenesis

Liu et al.,
a The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China b School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada c Department of Biology, University of Saskatchewan, Saskatoon S7N 5E2, Canada

... algorithm of the Basic Local Alignment Search Tool [25] hosted by the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov), and open reading frames were further analyzed using the gene prediction program FGENESH (Softberry Inc., Mount Kisco ...


Planta
Volume 238, Issue 2 , pp 293-305 DOI:10.1007/s00425-013-1891-3

Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives

Bimolata et al.,
1. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India 2. Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India

... Based on the sequences obtained from the genotypes under study, the coding regions and the UTR regions of the new alleles were predicted through the software utility, FGENESH (http://www.softberry.com) (Salamov and Solovyer 2000 ). ...


G3
March 1, 2013 vol. 3 no. 3 563-572 DOI:10.1534/g3.113.005587

Fine-Mapping and Identification of a Candidate Gene Underlying the d2 Dwarfing Phenotype in Pearl Millet, Cenchrus americanus (L.) Morrone

Parvathaneni et al.,
*Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602 †Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602

... respectively. The sequence of BAC 293B22 has been deposited in GenBank under accession number KC463796. Gene prediction was performed using FGENESH with the monocot training set (www.softberry.com). Repetitive ...


Theoretical and Applied Genetics
Volume 126, Issue 10 , pp 2643-2653 DOI:10.1007/s00122-013-2162-1

Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato

Zhang et al.,
1. The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People’s Republic of China 2. Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

... MapQTl 4.0 (Van Ooijen and Maliepaard 1996) was used to perform the QTl analysis. Gene prediction and sequence analysis The online program FGeneSH was used to pre- dict open reading frames (OrFs) in the target region (http://linux1.softberry.com/). ...


PloS one
September 24, 2013DOI: 10.1371/journal.pone.0075544

Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Wu et al.,
Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, China

... Repeats/ gene_annotation.pdf). Here, gene predictions were performed mainly by using the program FGENESH with training sets of the monocots including maize, rice, wheat and barley (http://www.softberry.com). In addition ...


Heredity
110, 570-577 (June 2013) | doi:10.1038/hdy.2013.2

Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays

Kanizay et al.,

... Masked contigs were then mapped with BLAST to the non-redundant nucleotide and protein databases at NCBI with an e-value cutoff of 10 ?5 (Supplementary Table 2). Gene models were identified using FGenesH (SOFTBERRY) and Augustus (http://bioinf.uni-greifswald.de ...


BMC Genomics.
2013; 14: 169. DOI:10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes

Gillespie et al.,
Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, 5 Portarlington Road, Geelong, Victoria, Australia 2School of Life and Environmental Sciences, Deakin University, Pigdons Road, Geelong, Victoria 3216, Australia

...The scaffolds of interest were then submitted to a Hidden Markov Model gene prediction program (FGENESH, Softberry; http://linux1.softberry.com/berry.phtml) using parameters for chicken (aves) to identify predicted full-length gene sequences. Where scaffolds were too large to be processed by FGENESH, the region of the scaffold with the BLAST match was submitted....


Molecular Biology Reports
Volume 40, Issue 2 , pp 1385-1396 DOI:10.1007/s11033-012-2182-y

Characterization of the NADP-malic enzymes in the woody plant Populus trichocarpa

Yu et al.,
1. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China

... We performed the PtNADP-ME4 gene structure (exons and introns) prediction using the FGENESH program on the SoftBerry server (http://www.soflberry.corn/berry.phtml), and present new predicted PtNADP-ME4 gene sequences (Table S1). ...


Front Plant Sci.
2013; 4: 318. DOI:10.3389/fpls.2013.00318

A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes

Perry et al.,
1Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada 2Department of Biological Sciences, University of Windsor, Windsor, ON, Canada

...The sequence data was examined for open reading frames using FGENESH (http://www.softberry.org), with the Medicago gene model....


New Phytologist
197: 595–605. doi: 10.1111/nph.12043

The Brassica napus blackleg resistance gene LepR3 encodes a receptor-like protein triggered by the Leptosphaeria maculans effector AVRLM1.

Larkan et al.,
1Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada 2School of Plant Biology, University of Western Australia, Crawley, WA, Australia 3The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia

... Identification, cloning and transformation of candidate gene. A B. rapa BAC spanning the LepR3 interval was annotated for gene content using fgenesh software (www.softberry. com) trained to 'Dicot plants (Arabidopsis)' to predict gene content. ...


Theoretical and Applied Genetics
Volume 126, Issue 8 , pp 2187-2196 DOI:10.1007/s00122-013-2128-3

Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor

Yuhong Li, Changlong Wen, Yiqun Weng
1. Horticulture College, Northwest A&F University, Yangling, 712100, China 2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA

... with preceding fragment. Gene prediction in target genomic DNA regions was performed with the computer program FGENESH (Salamov and Solovyev 2000) (http://sunl.softberry.com/) and checked manually. Candidate gene ...


The Plant Cell
July 2013 vol. 25 no. 7 2536-2544 DOI:10.?1105/?tpc.?113.?111856

Formation and Expression of Pseudogenes on the B Chromosome of Rye

Ali Mohammad Banaei-Moghaddam, Karla Meier, Raheleh Karimi-Ashtiyani and Andreas Houben 1
Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany

... Therefore, the genomic sequences of all fragments were BLASTed against the rye EST database (Haseneyer et al., 2011) and analyzed using FGENESH software (http://linux1.softberry.com/berry.phtml) (see Supplemental Figure 1 online). ...


Front Plant Sci.
2013; 4: 258. DOI:10.3389/fpls.2013.00258

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics

Studholme et al.,
1Biosciences, Molecular Plant Pathology, College of Life and Environmental Sciences, University of Exeter, Exeter, UK 2Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK Edited by: Corne M. J. Pieterse, Utrecht University, Netherlands

... (1991). Bioinformatics methods. We used Velvet version 1.1.04 (Zerbino and Birney, 2008) for de novo assembly of genome sequence. For ab initio gene prediction we used FgenesH (http://linux1.softberry.com/berry.phtml?topic=fgenesh). ...


Plant Science
Volume 210, September 2013, Pages 241–249 DOI:10.1016/j.plantsci.2013.06.003

Mutation of OsDET1 increases chlorophyll content in rice

Huang et al.,
a Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400030, China b Institute of Rice, Chongqing Academy of Agricultural Sciences, Chongqing, China

... mapped to a 87-kb DNA region (Fig. 1a). Eight annotated candidate genes were located in the DNA region using the program FGENESH 2.2 (www.softberry.com). Further amplification of the relevant DNA fragments and sequence ...


G3
January 1, 2013 vol. 3 no. 1 41-63 doi: 10.1534/g3.112.004044

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Manning et al.,
*Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 †Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4 ‡Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006

...Protein-encoding genes were annotated using a combination of manual curation, EST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com) and GENEID (http://genome.crg.es/software/geneid). ...


Physiological and Molecular Plant Pathology
Volume 84, October 2013, Pages 76–85 DOI:10.1016/j.pmpp.2013.07.007

Foatf1, a bZIP transcription factor of Fusarium oxysporum f. sp. cubense, is involved in pathogenesis by regulating the oxidative stress responses of Cavendish banana (Musa spp.)

Xingzhu Qi b, Lijia Guo a, c, Laying Yang a, c, Junsheng Huang a, c,
a Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China b College of Agriculture Hainan University, Haikou 570228, China c Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Haikou 571101, China

... The protein-encoding gene sequence was submitted to a gene-finding program (FGENESH A, Softberry Inc.) to perform automated annotation and obtain the putative mRNA sequence of Foatf1. The PCR primers were designed based on the putative mRNA sequence of Foatf1. ...


PloS one
December 16, 2013DOI: 10.1371/journal.pone.0082353

Mating Type Locus of Chinese Black Truffles Reveals Heterothallism and the Presence of Cryptic Species within the T. indicum Species Complex

Beatrice Belfiori, Claudia Riccioni, Francesco Paolocci, Andrea Rubini
Institute of Biosciences and BioResources - Perugia Division, National Research Council, Perugia, Italy

... www.geneious.com). Gene prediction analyses were performed using FGENESH (http://linux1.softberry.com/berry.phtml). RNA Isolation and Reverse-transcription Polymerase Chain Reaction Analysis. Total RNA was isolated ...


Plant Disease
February 2013, Volume 97, Number 2 Pages 245-251 http://dx.doi.org/10.1094/PDIS-11-11-0941-RE

Chromosomal Mapping and QTL Analysis of Resistance to Downy Mildew in Cucumis sativus

S. P. Zhang et al.,
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;

... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and veriWed by FGENESH (http://linuxl.softberry.com/) (40), GENESCAN (http://genes.mit.edu/ GENSCAN.html) (4), TwinScan (http:// mblab.wustl.edu/software/download/) (24), and then ...


Phytopathology
June 2013, Volume 103, Number 6 Pages 594-599 http://dx.doi.org/10.1094/PHYTO-10-12-0260-R

Functional Analysis of Pid3-A4, an Ortholog of Rice Blast Resistance Gene Pid3 Revealed by Allele Mining in Common Wild Rice

Qiming Lv et al.,
Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China

... 9-bp deletion, in addition to many SNPs, compared with that of Pid3. According to the computer program FGENESH (http://www.softberry.com), the two genes should have predicted promoter regions beginning 900-bp from their respective start codons, ...


BMC Plant Biology
2013, 13:162 doi:10.1186/1471-2229-13-162

Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize

Tao et al.,
1 National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China 2 Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, Iowa 50011, USA 3 Research Center Flakkebjerg, University of Aarhus, 4200, Slagelse, Denmark

... We used Fgenesh software (http://linux1.softberry.com/berry.phtml, version 2.6) to predict ten putative genes from the masked sequence, including seven genes with putative functions, two hypothetical genes, and one gene without significant similarity to known genes (Figure 3C ...


J Hered
(2013) 104 (2): 273-286. doi: 10.1093/jhered/ess102

Identification and Characterization of a Homologue to the Arabidopsis INDEHISCENT Gene in Common Bean

Tania Gioia, Giuseppina Logozzo, James Kami, Pierluigi Spagnoletti Zeuli and Paul Gepts
From the Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Universita degli Studi della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy (Gioia, Logozzo, Spagnoletti Zeuli); and the Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616–8780 (Kami and Gepts).

... with AtIND. Gene structure was predicted using the software FGENESH (http://linux1.softberry.com/berry.phtml), whereas the search for ORFs was performed using ORF finder (http://www.ncbi.nlm.nih.gov/projects/gorf/). To identify ...


J. Exp. Bot.
(2013) 64 (2): 651-663. doi: 10.1093/jxb/ers363

Identification of differentially methylated regions during vernalization revealed a role for RNA methyltransferases in bolting

Hebrard et al.,
1 Universite d’Orleans, UFR/Faculte des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328 ARCHE, rue de Chartres, BP6759, 45067 Orleans cedex 2, France 2 SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium

... The identification of potential transposable elements (TEs) in the RLGS genomic sequences was realized by the identification of potential coding sequences (FGENESH on http://linux1. softberry.com/berry.phtml) followed by BLASTP analysis and the search of dispersed ...


Ann Bot
(2013) 111 (2): 305-315. doi: 10.1093/aob/mcs260

A triallelic genetic male sterility locus in Brassica napus: an integrative strategy for its physical mapping and possible local chromosome evolution around it

Lu et al.,
1National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, China 2Dandong Academy of Agricultural Sciences, Fengcheng 118109, P.R. China

... Polymerase (Finnzymes Oy, Espoo, Finland). The website-based software FGENSH (http://www.softberry.com) was employed to predict the putative open reading frames (ORFs) located in the target region. The Plant Repeat Databases ...


Molecular Genetics and Genomics
December 2013 DOI:10.1007/s00438-013-0795-z

A systematic exploration of high-temperature stress-responsive genes in potato using large-scale yeast functional screening

Baniekal Hiremath Gangadhar, Jae Woong Yu, Kappachery Sajeesh, Se Won Park
1. Department of Molecular Biotechnology, Konkuk University, Seoul, 143701, South-Korea

... FGeneSH (http://linux1.softberry.com/berry.phtml?topic=fgenesh &group=programs&subgroup= gfind) was used for those sequences for which we could not able to find possible OrF using GenSCan (Burge and Karlin 1998; Salamov and Solovyev 2000). ...


Crop Science
27 Nov. 2013; doi: 10.2135/cropsci2013.09.0598

Fine Mapping of the Cross-incompatibility Locus Gametophytic Factor 1 (ga1) Using a Homogeneous Maize Population 2

Liu et al.,
1 State Key Laboratory of Crop Biology, Shandong Agricultural University, Daizong Street 61, Taian, Shandong, 271018, CHINA 2 College of Life Science, Shandong University, Shanda South Street 27, Jinan, 250100, CHINA

... polyacrylamide gel and visualized with ethidium bromide staining. The maize gene 18 set (www.maizeequence.org) and website-based software FGENSH 19 (http://www.softberry.com) was applied to predict and filter the putative genes from 20 the mapping interval. 21 22 ...


Appl. Environ. Microbiol.
June 2013 vol. 79 no. 12 3770-3778 DOI:10.1128/AEM.03833-12

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Aylward et al.,
Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAa Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USAb

... Amino acid sequences for the nucleotide sequences of these CAZyme genes were obtained using a combination of 6-frame translation, the software program FGENESH (Softberry), and BLASTX (27) against the NCBI NR database (44). ...


New Phytologist
197: 416–430. doi: 10.1111/nph.12026

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state.

Lafon-Placette et al.,
1Universite d'Orleans, Faculte des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Orleans, France 2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), Orleans, France

... Identification of transposase was performed using Fgenesh software (http://linux1.softberry.com/ berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) and confirmed by TBlastX analysis (e-value < 10 ?30 ) on a flowering plant transcripts database. ...


Genetics
September 1, 2013 vol. 195 no. 1 263-273 DOI:10.1534/genetics.113.152330

Cloning and Characterization of a Critical Regulator for Preharvest Sprouting in Wheat

Liu et al.,
*Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 †Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506 ‡Faculty of Science, Genomics and Biotechnology Section, Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia

... Bobwhite as control. Bioinformatics and statistical analysis. Genomic sequences from the three BACs covering the Qphs.pseru-3AS region were annotated using FGENESH (http://linux1.softberry.com/berry.phtml). The promoter ...


New Phytologist
200: 675–690. doi: 10.1111/nph.12414

A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis

Krokida et al.,
1Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, Greece 2Department of Metabolic Biology, John Innes Centre, Norwich, UK 3Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico

... A region of c. 300 kb flanking each side of the OSC genes was screened and analysed using FGENESH gene prediction software (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group= programs&subgroup=gfind) and GeneScanwebserver (Burge & Karlin, 1998). ...


BMC Genomics
2013, 14:683 doi:10.1186/1471-2164-14-683

A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids

Davey et al.,
1 Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium 2 Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia

... B-genome annotation. Ab initio gene prediction was carried out using the FGENESH software, available online from http://linux1.softberry.com/all.htm webcite and using the default parameters and the 'monocot model plant' parameters. ...


Acta Physiologiae Plantarum
Volume 35, Issue 2 , pp 483-500 DOI:10.1007/s11738-012-1091-y

Analysis of the expression, subcellular and tissue localisation of phosphoglucan, water dikinase (PWD/GWD3) in Solanum tuberosum L.: a bioinformatics approach for the comparative analysis of two ?-glucan, water dikinases (GWDs) from Solanum tuberosum L.

Orzechowski et al.,
1. Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland 2. Department of Biometrics and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland

... Identification of the coding region, open reading frames and the translation of the StGWD3 nucleotide sequence was based on the FGENESH gene structure prediction based on the Hidden Markov Model (HMM) constructed for Nicotiana tabacum (Solanaceae) genome (http://?linux1.?softberry.?com/?berry.?phtml). ...


Plant Molecular Biology Reporter
Volume 32, Issue 1 , pp 28-41 DOI:10.1007/s11105-013-0597-9

Genome-Wide Identification, Classification, Expression Profiling, and SSR Marker Development of the MADS-Box Gene Family in Citrus

Hou et al.,
1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China

... pseudogenes or incorrect annotations because of the lack of a start or stop codon in the open reading frame, and manual reannotation was performed to correct and reannotate the putative MADS-box using an online web server FGENESH (http://linux1.softberry.com/ berry.phtml ...


Planta
Volume 237, Issue 1 , pp 279-292 DOI:10.1007/s00425-012-1756-1

Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice

Zhou et al.,
1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China 2. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

... P0027G10. Within this region, five ORFs were predicted using the program FGENESH 2.2 (http://www. softberry.com) (Fig. 2b). To determine the mutation site, all five cDNA sequences were separately isolated from young leaves. ...


Fungal Diversity
May 2013, Volume 60, Issue 1, pp 161-170, DOI:10.1007/s13225-013-0228-7

Getting to the bottom of Taxol biosynthesis by fungi

Uwe Heinig, Susanne Scholz, Stefan Jennewein
1. Fraunhofer Institut fur Molekularbiologie und Angewandte Okologie, Forckenbeckstrasse 6, 52074, Aachen, Germany

... Sequence analysis Sequences were analyzed using CLC Combined Workbench v3.6.1, Lasergene 7 Package, NCBI Blast and CloneManager Professional Suite 8. FGENESH was use for ORF and protein prediction (http://linux1.softberry.com/). ...


Journal of Plant Interactions
Volume 8, Issue 1, 2013 pages 34-44 DOI:10.1080/17429145.2012.721523

Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races

Thakur et al.,
a National Research Centre on Plant Biotechnology , IARI , New Delhi , 110012 , India b Deparment of Biotechnology , Himachal Pradesh University , Shimla , 171005 , India

... BioEdit Software version 7.0.9.0 (www.mbio.ncsu.edu). Gene coding regions were predicted with FGENESH (www.softberry.com) using the Piz-t sequence as reference. The functional domain(s) which play an important role ...


Scientia Horticulturae
Volume 164, 17 December 2013, Pages 323–332 DOI:10.1016/j.scienta.2013.09.040

Transcriptional profile of differentially expressed genes related to abortive flower buds under short light period stress in petunia

Yue et al.,
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China

... 2.7. Sequence and bioinformatics analysis of Phms2. Through EST blast analysis in the genome database of petunia, we successfully predicted the full-length open reading frame (ORF) of Phms2 using the FGENESH tool (http://www.softberry.com). ...


Front Plant Sci.
2013; 4: 317. DOI:10.3389/fpls.2013.00317

In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr

Reinprecht et al.,
1Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada 2Department of Plant Sciences, North Dakota State University, Fargo, ND, USA Edited by: Georgina Hernandez, Universidad Nacional Autonoma de Mexico, Mexico Reviewed by: Alejandra A. Covarrubias, Universidad Nacional Autonoma de Mexico, Mexico; Steven B. Cannon, United States Department of Agriculture, USA

... The consensus sequence was analyzed for the presence of coding regions with GENSCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/) using Medicago truncatula and Arabidopsis, respectively as the model organisms. ...


ACS Chem. Biol.
2013, 8 (4), pp 741–748 DOI: 10.1021/cb3006787

Complexity Generation in Fungal Peptidyl Alkaloid Biosynthesis: A Two-Enzyme Pathway to the Hexacyclic MDR Export Pump Inhibitor Ardeemin

Stuart W. Haynes †, Xue Gao ‡, Yi Tang *‡§, and Christopher T. Walsh *†
† Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States ‡Department of Chemical and Biomolecular Engineering and §Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States

... Contigs containing candidate clusters were examined using eukaryotic gene predictor FGENESH (Softberry), and predicted proteins surrounding the candidate Ant-activating NRPS were examined by repeated BLAST search. ...


Theoretical and Applied Genetics
Volume 126, Issue 7 , pp 1825-1838 DOI:10.1007/s00122-013-2095-8

Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354

Anh-Tung Pham, Kaitlin McNally, Hussein Abdel-Haleem, H. Roger Boerma, Zenglu Li
1. Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA 2. Institute for Plant Biology, University of Zurich, Zurich, Switzerland 3. Georgia Seed Development Commission, Athens, GA, 30605, USA

... genes. In addition to using soybase's gene model, we also used the programs Fgenesh (http://linux1.softberry.com) and Expasy (http://web.expasy.org/cgi-bin/ translate/dna_aa) to predict gene structure and protein sequence. ...


Int. J. Mol. Sci.
2013, 14(7), 13559-13576; doi:10.3390/ijms140713559

First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant

Liu et al.,
1 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China 2 University of Chinese Academy of Sciences, Beijing 100039, China

... protein database (NR) [72]. Secondly, ab initio gene prediction was performed on the ENS dataset using the FGENESH feature (Dicot plants-Arabidopsis) of the MolQuest software package (softberry) [73]. Thirdly, a local BLAST ...


J. Integr. Plant Biol.
(2013) 55(7):643–653. DOI:10.1111/jipb.12068

Genome-wide analysis of the Sus gene family in cotton.

Zou et al.,
State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Sciences, Anyang, China

... DNA sequences or were predicted online using FGENESH (http://linux1.softberry.com/berry. phtml?topic=fgenesh&group=programs &subgroup=gfind). Predicted conserved domains were screened by SMART (http://smart.embl-heidelberg.de/) and ...


Experimental & Molecular Medicine
(2013) 45, e31; doi:10.1038/emm.2013.59

A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis

Park et al.,
1Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea 2Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea 3Department of General Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea

... indicating that our putative lincRNAs are not protein-coding genes: first, when we predicted open reading frames of our putative lincRNAs using gene prediction programs, such as GeneScan (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/), we ...


PloS one
February 01, 2013DOI: 10.1371/journal.pone.0055185

Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens

Liu et al.,
State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

... Gene Finding and Annotation. Gene models were predicted independently with a set of gene finders including Augustus [58], GeneMark-ES [59], GeneId [60] and SoftBerry eukaryotic gene finding suite (Fgenesh and Fgenesh+) [61]. ...


Journal of Integrative Plant Biology
Volume DOI:10.1111/jipb.12150

Auxin biosynthesis by the YUCCA6 flavin monooxygenase gene in woodland strawberry (Fragaria vesca)

Liu et al.,
1Forestry and Fruit Tree Research Institute, Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, China 2Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Biotechnology, SAAS, Shanghai, China 3Departamento de Biologia Moleculary Bioquimica, Universidad de Malaga, Malaga, Spain

... genes (Cheng et al. 2006) as query sequences. Hereafter, HMM-based gene structure prediction was carried out using the FGENESH program (default values) at http://linux1.softberry.com/berry.phtml. To confirm these candidates ...


BMC Genomics
2013, 14:60 doi:10.1186/1471-2164-14-60

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

Fellers et al.,
1 USDA-ARS, Hard Winter Wheat Genetics Research Unit, Department of Plant Pathology, Manhattan, KS, 66506, USA 2 Agriculture & Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, BC, V0H 1Z0, Canada

... Louis, MO. BAC clones were cultured, subcloned, shot gun sequenced, and assembled (Washington University Genome Center, St. Louis, MO). Gene calls were made using FGENESH with gene models specific to Puccinia (http://linux1.softberry.com/berry.phtml webcite;). ...


BMC plant biology
(2013). 13(1), 89. DOI:10.1186/1471-2229-13-89

Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer picea abies reveals extensive conservation as well as dynamic patterns.

Hedman, H., Zhu, T., von Arnold, S., & Sohlberg, J. J.
Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO-Box 7080, Uppsala, SE, 75007, Sweden

... Gene predictions were performed with FGENESH (http://linux1.softberry.com/berry.phtml) trained with dicot plants (Arabidopsis thaliana). Primer sequences are listed in Additional file 5. Gene and cDNA accessions are listed in Additional file 6. Phylogenetic analysis ...


ChemBioChem.
(2013). Volume 15, Issue 2, pages 284–292, January 24, 2014 DOI:10.1002/cbic.201300626

Identification of the First Diphenyl Ether Gene Cluster for Pestheic Acid Biosynthesis in Plant Endophyte Pestalotiopsis fici

Xu et al.,
1State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101 (China) 2Beijing Institute of Pharmacology & Toxicology, 27 Taiping Road, Haidian District, Beijing 100850 (China)

... the accession number KC145148. The ORFs were predicted from the sequence by using the GENSCAN Web Server at MIT (http://genes.mit.edu/GENSCAN.html) and FGENESH (Softberry). The deduced proteins of corresponding ...


BMC plant biology
(2013). 13(1), 126. DOI:10.1186/1471-2229-13-126

Molecular cloning and characterisation of SlAGO family in tomato

Xian et al.,
Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, People’s Republic of China

... After searching for AGO genes, bioinformatics tools, such as FGENESH (http://linux1.softberry. com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) was used to analyze and predict those unknown SlAGOs, and BLASTX of NCBI (http://blast.ncbi.nlm.nih.gov/Blast ...


BMC genomics
(2013). 14(1), 1-11. DOI:

Haplotype analysis of sucrose synthase gene family in three Saccharum species

Zhang, J., Arro, J., Chen, Y., & Ming, R.
(1)College of Life Sciences, Fujian Normal University, Fuzhou, 350108, China (2)Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

... For genomic sequences that had not previously been annotated, we supplemented the above methods with the use of Genscan (http://?genes.?mit.?edu/?GENSCAN.?html)[43] and FGENESH (http://?linux1.?softberry.?com/?berry.?phtml) gene prediction software....


International journal of molecular sciences
(2013). 14(11), 22462-22482. DOI:10.3390/ijms141122462

Cloning, Characterization and Effect of TmPGRP-LE Gene Silencing on Survival of Tenebrio Molitor against Listeria monocytogenes Infection

Tindwa et al.,
1 Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Korea 2 National Research Laboratory of Defense Proteins, College of Pharmacy, Pusan National University, Jangjeon Dong, Kumjeong Ku, Busan 609-735, Korea

... 1.0, NetOGlyc, NetPhos 2.0 and NetPhosK 1.0 server respectively (Technical University of Denmark, Lyngby, Denmark). The potential coding region was predicted using FGENESH (Softberry, Inc., Mount Kisco, NY, USA) [44]. ...


BMC microbiology
(2013). 13(1), 165. DOI:10.1186/1471-2180-13-165

Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae

Wight, W. D., Labuda, R., & Walton, J. D.
1 Department of Energy Plant Research Laboratory, Michigan State University, 612 Wilson Road, Room 210, East Lansing, MI 48824, USA 2 Romer Labs Division Holding GmbH, Technopark 1, Tulln 3430, Austria

... Page 14. (http://www.ebi.ac.uk/Tools/msa/clustalw2/), and SPIDEY (NCBI). Assembly of predicted protein sequences was performed using DNASTAR Lasergene software with assistance from FGENESH (www.softberry.com) with Alternaria as the training model. ...


BMC genomics
(2013). 14(1), 335. DOI:10.1186/1471-2164-14-335

Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae

Lin, X., Zhang, Y., Kuang, H., & Chen, J.
Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, P.R. China

... 3,110 protein sequences with ATP binding domain and 6,979 protein sequences with LRR domain from NCBI was used to verify the potential NBS- LRR or LRR-LRK encoding genes [3]. All identified sequences were annotated using FGENESH [www.softberry.com] and ...


BMC genomics
(2013). 14(1), 109. DOI:

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

Wan, H., Yuan, W., Bo, K., Shen, J., Pang, X., & Chen, J.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China

...the upstream and downstream of BLAST hits, were annotated using the FGENESH...


PloS one
(2013). 8(4), e62288. DOI:10.1371/journal.pone.0062288

Genome-Wide Expression Analysis of Soybean MADS Genes Showing Potential Function in the Seed Development

Fan et al.,
MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China

... The fragment genes were predicted the whole CDS by FGENESH (http://linux1.softberry.com/berry.phtml) or blasting the NCBI Ref-RNA database (Table S1)....


Mobile DNA
(2013). 4(1), 12.

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

Bao, W., & Jurka, J.
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA

... The TE-encoded multiple-exon genes were predicted by FGENESH program (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind), ...


BMC genomics
(2013). 14(1), 79. DOI:10.1186/1471-2164-14-79

Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics

Ksiazkiewicz et al.,
1 Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland 2 Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland

...BAC sequences with masked repetitive regions were subjected to FGENESH [42,43]in silico gene prediction followed by BLAST against the EST, nr, and Swiss-Prot [44] c...


FGENESH 2012

Nature Genetics
2012 44, 1060–1065. doi:10.1038/ng.2372

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.

O'Connell et al.,
Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany. Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiologia y Genetica, Universidad de Salamanca, Villamayor, Spain.

...Gene structures were predicted using the Broad Institute automated gene-calling pipeline35 based on a combination of gene models predicted by the programs FGENESH (Softberry Inc., USA), GENEID36, GeneMark37, SNAP38 and Augustus39 together with EST-based and manually curated gene models. GENEID, FGENESH, SNAP and Augustus were trained using a set of high-confidence EST-based gene models generated by clustering Blat-aligned species-specific ESTs....


J. Exp. Bot.
(2012) 63 (1): 203-214. doi: 10.1093/jxb/err264

Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress

Lichao Zhang, Guangyao Zhao, Jizeng Jia, Xu Liu and Xiuying Kong *
The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

... Only the sequences that shared >95% matches were considered redundant. The open reading frames (ORFs) were predicted using FGENESH (http://www.softberry.com) and were translated into amino acid sequences. Finally ...


Applied Microbiology and Biotechnology
June 2012 DOI 10.1007/s00253-012-4130-0

Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides

Suqin Yin, Xia Yu, Qing Wang, Xiao-Qing Liu, Shu-Ming Li
1. College of Life Sciences, Capital Normal University, No.105 Xisanhuan Beilu, Beijing, 100048, China 2. Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037, Marburg, Germany

... Computer-assisted sequence analysis FGENESH (Softberry, Inc.) and the DNASIS software pack- age (version 2.1: Hitachi Software Engineering, San Bruno, CA) were used for intron prediction and sequence analysis, respectively. ...


Journal of Industrial Microbiology & Biotechnology
June 2012, Volume 39, Issue 6, pp 869-876 DOI: 10.1007/s10295-012-1087-z

High-level expression of a novel Penicillium endo-1,3(4)-b-d-glucanase with high specific activity in Pichia pastoris

Chen et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China

... respectively. The cod- ing region was predicted online using the FGENESH program (http://linux1.softberry.com/berry.phtml/). SignalP 4.0 web server (http://www.cbs.dtu. dk/services/SignalP/) was used to predict the signal peptide. ...


Immunogenetics
DOI: 10.1007/s00251-012-0672-7

Immunoglobulin genes of the turtles

Susana Magadan-Mompo, Christian Sanchez-Espinel & Francisco Gambon-Deza
Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain Shared Unit of Immunology, Vigo University Hospital Complex (Hospital Meixoeiro), University of Vigo, Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As Lagoas-Marcosende, Vigo 36310, Pontevedra, Spain

... Identification of the exons coding for the constant heavy (CH) domains was performed using the software FGENESH (www.softberry.com) (Solovyev et al. 2006; Yao et al. ...


Advances in Environment, Computational Chemistry and Bioscience
ISBN: 978-1-61804-147-0

In silico study of non-coding, coding transcription region and domain interaction for chromosomal translocation sequences

PRAVEEN KUNAR KORLA 1, SHAN-CHIH LEE 2 , JIM SHEU 3, JACK CHENG 3, KA-LOK NG 1
1 Department of Biomedical Informatics,Asia University, Taichung,TAIWAN 41354 2 School of Medical Imaging and Radiological Sciences, Chung Shan Medical University, Taichung, TAIWAN 40201

... The URL addresses for these web based tools are;Fgenesh (http://linux1.softberry.com/berry. phtml), Genemark (http://exon.gatech.edu/eukhmm.cgi), Genscan (http://immunax.dfci.harvard. edu/Tools/genscan.ht ml) and Webgene (http://zeus2.itb.cnr.it/~webgene/genebuilder.html ...


Cereal Research Communications
Volume 40, Number 3/September 2012 pp. 362-372 DOI: 10.1556/CRC.40.2012.3.5

Molecular mapping of quantitative trait loci for flag leaf length and other agronomic traits in rice (Oryza sativa)

Sonah et al.,
1 National Research Centre on Plant Biotechnology New Delhi 110012 India 2 Directorate of Rice Research Hyderabad AP India

... sativa subsp. japonica cv. Nipponbare (http://rice.plantbiology.msu.edu/) was used for gene prediction. FGENESH gene prediction software (www.softberry.com) was used to predict genes in this sequence. Predicted genes ...


Animal Science Journal
Volume 83, Issue 5, pages 386–393, May 2012 DOI: 10.1111/j.1740-0929.2011.00975.x

Predictive mutational bioinformatic analysis of variation in the skin and wool associated corneodesmosin (CDSN) gene in sheep

SUBRAMANIAM et al.,
1 Western Australian Biomedical Research Institute (WABRI) & Centre for Health Innovation Research Institute (CHIRI), School of Biomedical Sciences, Curtin University, Perth 2 School of Biological Sciences, Murdoch University, Murdoch, Australia

... Gene prediction tools such as GENSCAN (Burge & Karlin 1997), FGENESH (http://www.softberry.com), HMM gene (http://www.cbs.dtu.dk/services/HMMgene/), Augus- tas (Stanke et al. 2006) and GeneMark (Lomsadze et al. ...


Mol Biol Evol
(2012) 29 (2): 861-871. doi: 10.1093/molbev/msr261 First published online: October 14, 2011

Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes

Jian-Hong Xu 1,†, Jeffrey L. Bennetzen 2 and Joachim Messing 1
1 Waksman Institute of Microbiology, Rutgers, The State University of New Jersey 2 Department of Genetics, University of Georgia

... About 100 kb–1 Mb chromosomal regions of alpha setarin gene loci were annotated by Fgenesh software (http://linux1.softberry.com/berry.phtml) for gene models, and repeats sequences were masked by Repeatmasker (http://www.repeatmasker.org/). ...


Archives of Insect Biochemistry and Physiology
Volume 79, Issue 2, pages 87–103, February 2012 DOI: 10.1002/arch.21014

ANNOTATION AND EVOLUTION OF THE ANTIOXIDANT GENES IN THE SILKWORM, Bombyx mori

Gui-Qin Shi 1, Quan-You Yu 1, Ze Zhang 1,2
1The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing, China 2The Key Sericultural Laboratory of the Agricultural Ministry of China, Southwest University, Chongqing, China

... If some genome sequences showed even weak sequence similarity to any query sequences, their flanking regions (1 kb or more long) were manually extracted, and then put them into Softberry database to predict new genes using FGENESH program. ...


Journal of Microbiological Methods
Volume 91, Issue 3, December 2012, Pages 412–419 DOI: 10.1016/j.mimet.2012.09.014

Rapid screening of an ordered fosmid library to clone multiple polyketide synthase genes of the phytopathogenic fungus Cladosporium phlei

Kum-Kang So et al.,
a Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Chonbuk 561-756, Republic of Korea b Department of Bio-Environmental Chemistry, Wonkwang University, Iksan, Chonbuk 570-749, Republic of Korea

... The structures of putative PKS genes and proteins were determined using FGENESH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) and INTERPROSCAN (http://www.ebi.ac.uk/Tools/pfa/iprscan/), respectively. ...


Fungal Genetics and Biology
Volume 49, Issue 12, December 2012, Pages 977–986 DOI: 10.1016/j.fgb.2012.08.008

Reproductive mode and life cycle of the ash dieback pathogen Hymenoscyphus pseudoalbidus

A. Gross a, P.L. Zaffarano a, A. Duo a, C.R. Grunig b,
a Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitatsstrasse 16, 8092 Zurich, Switzerland b Microsynth AG, Schutzenstrasse 15, 9436 Balgach, Switzerland

... Initial sequence analysis was conducted with the basic local alignment search tool (BLAST, http://blast.ncbi.nlm.nih.gov/Blast.cgi) and refined by the gene structure prediction program FGENESH (http://linux1.softberry.com/berry.phtml) using the matrices of Sclerotinia ...


Applied Microbiology and Biotechnology
August 2012, Volume 95, Issue 4, pp 947-955 DOI: 10.1007/s00253-011-3807-0

A novel thermoacidophilic and thermostable endo-b-1,4-glucanase from Phialophora sp. G5: its thermostability influenced by a distinct b-sheet and the carbohydrate-binding module

Zhao et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People’s Republic of China

... ncbi.nlm.nih.gov/BLAST/), respectively. Introns, exons, and transcription initiation sites were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted using SignalP (http://www. cbs.dtu.dk/services/SignalP/). ...


The FASEB Journal
Published online before print September 20, 2012 DOI: 10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK;

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH (http://linux1.softberry.com/), Wise2 (http:// www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/ GENSCAN.html). Mosquito rearing and mating analysis ...


Journal of Zhejiang University SCIENCE B
June 2012, Volume 13, Issue 6, pp 452-464 DOI: 10.1631/jzus.B1100338

Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae

Ping Li, Bin Bai, Hong-yan Zhang, Heng Zhou, Bo Zhou
1. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China 2. Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China

... The Page 3. Li et al. / J Zhejiang Univ-Sci B (Biomed & Biotechnol) 2012 13(6):452-464 454 BAC sequence was annotated by using gene predic- tion program and homology search. The Fgenesh program (http://www.softberry.com) was used for gene prediction. ...


Journal of Bioscience and Bioengineering
Volume 113, Issue 6, June 2012, Pages 710–714 DOI: 10.1016/j.jbiosc.2012.02.005,

Cloning, over-expression and characterization of an alkali-tolerant endo-b-1,4-mannanase from Penicillium freii F63

Wang et al.,
1 Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China 2 Engineering Research Centre for the Protection and Utilization of Bioresource in Southern China, College of Life Science, South-Central University for Nationalities, Wuhan 430074, PR China

... The online software FGENESH (http://linux1.softberry.com/berry.phtml) was used to predict introns, exons and transcription initiation sites of the DNA sequence. The signal peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...


New Phytologist
Volume 193, Issue 4, pages 1049–1063, March 2012 DOI: 10.1111/j.1469-8137.2011.04006.x

Tracing the origin and evolutionary history of plant nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes

Jia-Xing Yue 1,2, Blake C. Meyers 3, Jian-Qun Chen 1, Dacheng Tian 1, Sihai Yang 1
1 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China 2 Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005, USA

... In addition, the nucleotide sequences of these two genes, together with their 5? and 3? flanking regions (each 5000 bp, respectively), were used for re-annotation with FGENESH (http://linux1.softberry.com/berry.phtml) and the domain architecture of the resulting predicted ...


PLoS ONE 7
(7): e40564. doi:10.1371/journal.pone.0040564

Identification of a Polyketide Synthase Required for Alternariol (AOH) and Alternariol-9-Methyl Ether (AME) Formation in Alternaria alternata

Saha et al.,
Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany Department of Food Chemistry, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany

... A. alternata. Intron-exon borders were predicted using FGENESH (softberry.com) trained on A. brassicicola gene models but have not yet been verified experimentally due to the rather large nature of PKS genes. Among these ...


Gene
Volume 500, Issue 1, 25 May 2012, Pages 73–79 DOI: 10.1016/j.gene.2012.02.051

Two novel N-terminal coding exons of Prkar1b gene of mouse: Identified using a novel approach of in silico and molecular biology techniques

Abdul Rouf Banday, Shafquat Azim, Sayeed Ur Rehman, Mohammad Tabish
Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India

... and Borodovsky, 1998) and is available at http://www.cbs.dtu.dk/services/HMMgene, Genescan (http://genes.mit.edu/GENSCAN.html), GeneSplicer available at http://cbcb.umd.edu/software/ GeneSplicer/ (Pertea et al., 2001), and FGENESH (http://www.softberry.com/berry.phtml ...


Developmental & Comparative Immunology
Volume 38, Issue 1, September 2012, Pages 1–9 DOI: 10.1016/j.dci.2012.03.001

Snakes antibodies

Francisco Gambon-Deza a, Christian Sanchez-Espinel b, Serafin Mirete-Bachiller a, Susana Magadan-Mompo c
a Servicio Gallego de Salud (SERGAS) Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain b Shared Unit of Immunology, University of Vigo – Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As Lagoas-Marcosende, Vigo 36310, Pontevedra, Spain

... previously published reptile immunoglobulin mRNAs. Limits were deduced following instructions in the software FGENESH (http://www.softberry.com) and Augustus (http://www.augustus.gobics.de/submission). In Additional File A ...


Bioresource Technology
Volume 130, February 2013, Pages 161–167 DOI: 10.1016/j.biortech.2012.12.067

Characterization of three novel thermophilic xylanases from Humicola insolens Y1 with application potentials in the brewing industry

Yanlong Du et al.,
a Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China b College of Biological Science and Engineering, Bei Fang University of Nationalities, Yinchuan 750021, PR China

... The sequence assembly was performed using the Vector NTI Advance 10.0 software (Invitrogen). Genes, introns, exons and transcription initiation sites were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...


Molecular Plant Pathology
Volume 13, Issue 9, pages 1089–1100, December 2012 DOI: 10.1111/j.1364-3703.2012.00818.x

Degradation of aromatic compounds through the b-ketoadipate pathway is required for pathogenicity of the tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici

Caroline B. Michielse 1,†,*, Linda Reijnen 1,‡, Chantal Olivain 2, Claude Alabouvette 2, Martijn Rep 1
1Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands 2UMR 1229 INRA, Universite de Bourgogne Microbiologie du Sol et de l'Environnement, Dijon, France

... 1996). The annotated FOXG_17757 gene lacks a 5' and 3' end. In this article, we suggest a new gene model based on fgenesh and augustus gene prediction software (http://www.softberry.com, http://augustus.gobics.de/). This ...


Theoretical and Applied Genetics
May 2012, Volume 124, Issue 7, pp 1173-1182 DOI: 10.1007/s00122-011-1777-3

Localization of high level of sequence conservation and divergence regions in cotton

Wang et al.,
1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

... hmm (Brudno et al. 2003), GENSCAN (Lomsadze et al. 2005) and FGENESH (http://linux1.soft- berry.com). The predicted genes were confirmed using BLASTN queries against the cotton EST database. To annotate genes, predicted ...


Genes & genomics
2012, vol. 34, no4, pp. 379-390

The NPR1 family of transcription cofactors in papaya: insights into its structure, phylogeny and expression

Santy et al.,
(1) Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan (CICY), C. 43, No. 130, Col. Chuburna de Hidalgo, Merida, Yucatan, Mexico

... Page 3. Genes & Genomics 1997). The open reading frames (ORFs) in the papaya DNA contigs harboring NPR1 homologues were predicted by the FGENESH program with the A. thaliana genome set as refer- ence (http://linux1.softberry.com/berry.phtml). ...


Applied Microbiology and Biotechnology
November 2012, Volume 96, Issue 4, pp 951-962 DOI: 10.1007/s00253-012-3873-y

Expression and characterization of a novel metagenome-derived cellulase Exo2b and its application to improve cellulase activity in Trichoderma reesei

Geng et al.,
1. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China 2. Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China

... The resulting reads were assembled using Newbler version 2.0 (http://www.454.com). ORFs in the assembled sequences were predicted by FGENESB (Softberry, Goteborg, Sweden) and a BLASTX search performed against the NR database to access annotation information. ...


ChemBioChem
Volume 13, Issue 17, pages 2583–2592, November 26, 2012 DOI: 10.1002/cbic.201200523

Identification of the Verruculogen Prenyltransferase FtmPT3 by a Combination of Chemical, Bioinformatic and Biochemical Approaches

Kathrin Mundt 1, Beate Wollinsky 1, Prof. Dr. Han-Li Ruan 2, Assoc. Prof. Dr. Tianjiao Zhu 3, Prof. Dr. Shu-Ming Li1
1Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, 35037 Marburg (Germany) 2Huazhong University of Science and Technology, Faculty of Pharmacy, Tongji Medical College and Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Hongkong Road 13, 430030, Wuhan (China)

... Computer-assisted sequence analysis: The DNASIS software package (version 2.1; Hitachi Software Engineering, San Bruno, CA) and FGENESH (Softberry, Inc.; http://www.softberry.com/ berry.phtml) were used for intron prediction and sequence analysis, respectively. ...


Molecular Genetics and Genomics
May 2012, Volume 287, Issue 5, pp 373-388 DOI: 10.1007/s00438-012-0682-z

Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa

Jin A. Kim et al.,
1. Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration, 224 Suinro Gwonseon-gu, Suwon, Gyeonggi-do, 441-707, Republic of Korea 2. National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea

... gov/BLAST/) were used when needed. Gene annotation was achieved using the Web-based gene-prediction program FGENESH Arabid- opsis (http://www.softberry. com/berry.phtml). A phylogenetic tree was constructed using ...


FEBS Journal
Volume 279, Issue 4, pages 572–585, February 2012 DOI: 10.1111/j.1742-4658.2011.08446.x

Identification and expression analysis of three novel splice variants of protein kinase A catalytic b subunit gene in the mouse using combinatorial in silico and molecular biology approaches

Abdul R. Banday, Shafquat Azim, Mohammad Tabish
Department of Biochemistry, Faculty of Life Sciences, AM University, Aligarh, India

... The FGENESH tool (http://www.softberry.ru/berry.phtml) was used for defining the structural features of gene under study. The ... sequence motifs/rules [53,54]. FEX tool (http://www.softberry.ru/berry.phtml) was used for validation of new ...


Theoretical and Applied Genetics
August 2012, Volume 125, Issue 4, pp 715-729 DOI: 10.1007/s00122-012-1863-1

Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents

Qingyong Yang et al.,
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

... The nonredundant sequences resulted from the hits were then collected and compared with known FAD2 and FAD3 genes in Arabidopsis . The program FGENESH (HMM-based gene structure prediction tool) was used for gene prediction (http:// www.softberry.com/). ...


Molecular Biology Reports
April 2012, Volume 39, Issue 4, pp 3375-3383 DOI: 10.1007/s11033-011-1108-4

Differentially expressed three non-coding alternate exons at 5? UTR of regulatory type I beta subunit gene of mouse

Abdul Rouf Banday, Shafquat Azim, Mohammad Tabish
1. Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, UP, 202002, India

... Gene/ Exon finding tools were used at HMMgene (http://www.cbs. dtu.dk/services/HMMgene), Genescan (http://genes.mit.edu/ GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/software/ GeneSplicer/), FGENESH (http://www.softberry.com/berry. phtml). ...


Canadian Journal of Microbiology
2012, 58(7): 815-827, DOI: 10.1139/w2012-054

Gene cloning, molecular modeling, and phylogenetics of serine protease P32 and serine carboxypeptidase SCP1 from nematophagous fungi Pochonia rubescens and Pochonia chlamydosporia

Eduardo Larriba, a,c Jose Martin-Nieto, b,c Luis Vicente Lopez-Llorca a,c
aDepartment of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, E-03080 Alicante, Spain. bDepartment of Physiology, Genetics and Microbiology, University of Alicante, P.O. Box 99, E-03080 Alicante, Spain.

... lyon1.fr/cap3.php. Gene prediction was made using FGENESH/HMM based on Neurospora genes (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group= programs&subgroup =gfind). Pairwise alignments were carried ...


PNAS
August 7, 2012 vol. 109 no. 32 E2155-E2164 DOI: 10.1073/pnas.1117982109

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

Zhengjun Xia et al.,
aNortheast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; bSoybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan;

... 2 B and C). A single intron-free gene (AB552962, 525 bp, 174 aa) was consistently identified by GenScan (45), GeneMark (46), FGENESH (http://linux1.softberry.com/berry.phtml), and RiceGAAS (44) for the dominant E1 genotype (Misuzudaizu and Harosoy-E1), and was ...


Comparative and Functional Genomics
Volume 2012 (2012), Article ID 914843, 14 pages doi:10.1155/2012/914843

In Silico Identification and Comparative Genomics of Candidate Genes Involved in Biosynthesis and Accumulation of Seed Oil in Plants

Arti Sharma and Rajinder Singh Chauhan
Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan 173 215, India

... Rapa, and soybean sequences were further annotated for gene models (open reading frames, including the 5?UTRs and 3?UTRs) using gene prediction algorithms of FGenesH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) [43– ...


Genetics
August 17, 2012 genetics.112.144436 DOI:10.1534/genetics.112.144436

High Throughput Discovery of Mutations in tef Semi-dwarfing Genes by Next Generation Sequencing Analysis

Qihui Zhu et al.,
1 University of Georgia; 2 Purdue University

... The complete clone sequences were submitted to GenBank (Accession numbers: JN672669-JN672670). The fosmid sequences were initially annotated by FGENESH (http://www.softberry.com) and GENESCAN (Buger and Karlin 1997). Putative proteins ...


Theoretical and Applied Genetics
November 2012, Volume 125, Issue 7, pp 1525-1537 DOI: 10.1007/s00122-012-1931-6

Development of candidate gene markers associated to common bacterial blight resistance in common bean

Chun Shi et al.,
1. Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, Harrow, ON, N0R 1G0, Canada 2. Department of Plant Agriculture, University of Guelph, Crop Science Building, Guelph, ON, N1G 2W1, Canada

... for Bio- technology Information (NCBI) database. Gene predictions were based on ab initio method by FGENESH software using Medicago gene model (http://www. softberry.com). Sequences were subjected to BlastN similarity ...


Mol Genet Genomics.
2012 Oct;287(10):765-84. Epub 2012 Aug 24.

Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution

Mun JH et al.,
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea

... Since the draft B. rapa genome did not provide information on the 50- and 30-UTR regions of the gene models, we used in-house trained FGENESH (www. softberry.com) to predict the 50- and 30-UTR regions of the BrARF genes. ...


PLoS ONE
7(9): e45307. doi:10.1371/journal.pone.0045307

Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae.

Cockram et al.,
1 John Bingham Laboratory, National Institute of Agricultural Botany, Huntington Road, Cambridge, United Kingdom, 2 Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, 3 Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Jena, Germany, 4 Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom

... helmholtz-muenchen.de/plant/triticeae/) or fl-cDNAs [40]. De novo gene predictions and reassessments were conducted using FGENESH (http://www.softberry.com/) using 'monocot' as the basis of gene prediction. Homology ...


PLoS ONE
7(9): e45307. doi:10.1371/journal.pone.0045307

Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae

Cockram et al.,
John Bingham Laboratory, National Institute of Agricultural Botany, Huntington Road, Cambridge, United Kingdom Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

...De novo gene predictions and reassessments were conducted using FGENESH (http://www.softberry.com/) using ‘monocot’ as the basis of gene prediction. ...


African Journal of Biotechnology
Vol. 11(77), pp. 14123-14131, 25 September, 2012 DOI: 10.5897/AJB12.778

Molecular cloning and characterization of an acyl-ACP thioesterase gene (AhFatB1) from allotetraploid peanut (Arachis hypogaea L.)

Wen Qigen, Lei Yong, Huang Jiaquan, Jiang Huifang and Liao Boshou
Oil Crop Research, Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, P. R. China.

... The theoretical molecular weight and isoelectric point of deduced polypeptide were predicted using the ProtParam program (http://www.expasy.ch/tools/protparam.html), and Exon-Intron analysis was made with the FGENESH program (http://linux1.softberry.com/). ...


Molecular Genetics and Genomics
March 2012, Volume 287, Issue 3 , pp 189-203 DOI: 10.1007/s00438-011-0671-7

Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato

Rahul Kumar, Manoj K. Sharma, Sanjay Kapoor, Akhilesh K. Tyagi, Arun K. Sharma
1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India 2. Department of Plant Pathology, University of California, Davis, CA, 95616, USA

... Gene structure of these BAC sequences was predicted using FGENESH (http://linux1. softberry.com/berry.phtml?topic=fgenesh& group=programs&subgroup=gfind) and 2 kb sequences upstream to predicted open reading frames were extrac- ted. ...


Molecular Biology Reports
Volume 40, Issue 2 , pp 1385-1396 DOI: 10.1007/s11033-012-2182-y

Characterization of the NADP-malic enzymes in the woody plant Populus trichocarpa

Yu et al.,
1. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China

... We performed the PtNADP-ME4 gene structure (exons and introns) prediction using the FGENESH program on the SoftBerry server (http://www.soflberry.corn/berry.phtml), and present new predicted PtNADP-ME4 gene sequences (Table S1). ...


Plant Disease
February 2013, Volume 97, Number 2 Pages 245-251 http://dx.doi.org/10.1094/PDIS-11-11-0941-RE

Chromosomal Mapping and QTL Analysis of Resistance to Downy Mildew in Cucumis sativus

Zhang et al.,
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Guizhou University, Guiyang 550025, China

... Only matches with an identity of ? 95% were retained. Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and veriWed by FGENESH (http://sunl.softberry. com/) (40), GENESCAN (http://genes.mit.edu/GENSCAN.html) (4), TwinScan ...


PLoS ONE
7(12): e53401. doi:10.1371/journal.pone.0053401

A Novel Family of Terminal-Repeat Retrotransposon in Miniature (TRIM) in the Genome of the Red Harvester Ant, Pogonomyrmex barbatus

Yihong Zhou, Sara Helms Cahan
Department of Biology, University of Vermont, Burlington, Vermont, United States of America

... assembly. Elements along with their flanking sequences were submitted to FGENESH program (Softberry, Inc., http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&subgroup=gfind) for gene prediction. ...


J Hered
(2012) doi: 10.1093/jhered/ess102

Identification and Characterization of a Homologue to the Arabidopsis INDEHISCENT Gene in Common Bean

Gioia T, Logozzo G, Kami J, Zeuli PS, Gepts P.
From the Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Universita degli Studi della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy (Gioia, Logozzo, Spagnoletti Zeuli); and the Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616–8780 (Kami and Gepts).

... with AtIND. Gene structure was predicted using the software FGENESH (http://linux1.softberry.com/berry.phtml), whereas the search for ORFs was performed using ORF finder (http://www.ncbi.nlm.nih.gov/projects/gorf/). To identify ...


Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 223-234 DOI: 10.1007/s00122-012-1827-5

Map-based cloning of a recessive genic male sterility locus in Brassica napus L. and development of its functional marker

Li et al.,
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China 2. Institute of Industrial Crops, Henan Academy of Agricultural Science, Zhengzhou, 450002, China

... Gene prediction and plant transformation The website-based software FGENESH (http://www.soft berry.com) was applied to predict the putative ORF from the candidate region. The genomic or coding sequences of predicted genes were submitted to NCBI (http://www.ncbi. ...


New Phytologist
Volume 197, Issue 2, pages 416–430, January 2013 DOI: 10.1111/nph.12026

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state

Lafon-Placette et al.,
1Universite d'Orleans, Faculte des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Orleans, France 2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), Orleans, France

... Identification of transposase was performed using Fgenesh software (http://linux1.softberry.com/ berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) and confirmed by TBlastX analysis (e-value < 10 ?30 ) on a flowering plant transcripts database. ...


BMC Genomics
2012, 13:409 http://www.biomedcentral.com/1471-2164/13/409

Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species

Diro Terefe-Ayana, Helgard Kaufmann, Marcus Linde and Thomas Debener
Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Str. 2, Hannover 30419, Germany

... Gene prediction and annotation based on the completely assembled sequence was carried out using the gene prediction program FGENESH (http://www.softberry.com). ...


Journal of Plant Interactions
Volume 8, Issue 1, 2013 pages 34-44 DOI: 10.1080/17429145.2012.721523

Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races

Thakur et al.,
a National Research Centre on Plant Biotechnology, IARI, New Delhi, 110012, India b Deparment of Biotechnology, Himachal Pradesh University, Shimla, 171005, India

... [CrossRef], [PubMed], [Web of Science ®], [CSA] View all references) and manually edited using BioEdit Software version 7.0.9.0 (www.mbio.ncsu.edu). Gene coding regions were predicted with FGENESH (www.softberry.com) using the Piz-t sequence as reference. ...


Mycology: An International Journal on Fungal Biology
Volume 3, Issue 1, 2012 pages 54-64 DOI: 10.1080/21501203.2011.654353

Two arginine biosynthesis genes are essential for pathogenicity of Colletotrichum higginsianum on Arabidopsis

Hiroyuki Takahara ab*, Aurelie Huser b & Richard O'Connell b
a Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan b Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Cologne, Germany

... 2007) and the FGENESH prediction tool using Fusarium and Magnaporthe matrices (Softberry Inc., Mount Kisco, NY, USA). Sequence homology searches were performed against the NCBI nr protein data base using appropriate BLAST algorithms. ...


PLoS ONE
7(9): e44264. doi:10.1371/journal.pone.0044264

Identification and Sequence Analysis of Metazoan tRNA 3?-End Processing Enzymes tRNase Zs.

Wang et al.,
Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China

... The splicing pattern was verified using the Fgenesh and Fgenesh_GC programs provided at the Softberry website (http://linux1.softberry.com/berry.phtml??topic=fgenesh). ...


Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 211-222 DOI: 10.1007/s00122-012-1826-6

Exploiting comparative mapping among Brassica species to accelerate the physical delimitation of a genic male-sterile locus (BnRf) in Brassica napus

Yanzhou Xie et al.,
1. National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement (Wuhan Branch), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China 2. College of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

... Biosystems, Foster City, CA, USA). Software packages FGENESH (http://www.softberry. com) and Glim- merHMM (Majoros et al. 2004) were both applied to pre- dict the putative ORF from the candidate region. The genomic or coding ...


Planta
Volume 237, Issue 1 , pp 279-292 DOI: 10.1007/s00425-012-1756-1

Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice

Kunneng Zhou et al.,
1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China 2. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

... P0027G10. Within this region, five ORFs were predicted using the program FGENESH 2.2 (http://www. softberry.com) (Fig. 2b). To determine the mutation site, all five cDNA sequences were separately isolated from young leaves. ...


PLoS ONE
7(12): e52293. doi:10.1371/journal.pone.0052293

Full-Length Minor Ampullate Spidroin Gene Sequence.

Chen et al.,
Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People's Republic of China Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

... Fgenesh 2.6 (http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup=gf?ind) was used for intron prediction. ...


BMC Plant Biology
2012, 12:85 DOI: 10.1186/1471-2229-12-85

Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns

Chen et al.,
1 School of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China

... As the absence of the cDNA sequence, the exon/intron structure of GaSus2 was predicted online using the FGENESH algorithm (http://linux1.softberry.com/berry.phtml), which resulted in the definition of 10 putative introns within its putative coding regions. ...


Genomics
Volume 99, Issue 4, April 2012, Pages 241–245 DOI:10.1016/j.ygeno.2012.01.007

Evolutionary genomics reveals the premetazoan origin of opposite gating polarity in animal-type voltage-gated ion channels

Xinjiang Cai
Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA Department of Molecular Pathogenesis, New York University Langone Medical Center, New York, NY 10016, USA

... In cases when TBlastN searches identified putative genes of interest that had not been annotated, or when currently annotated genes in the databases were believed to be incomplete, GeneMark.hmm and FGENESH programs (http://www.softberry.com/berry.phtml?topic ...


BMC Genomics
2012, 13:253 doi:10.1186/1471-2164-13-253

Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)

Chai et al.,
1 Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China 2 Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA

... Subsequently, manual reannotation was performed to correct the putative CCCH sequences using online web server FGENESH (http://linux1.softberry.com/berry.phtml webcite). In this endeavor, 12 protein sequences were corrected for further analysis. ...


ChemBioChem
Volume 13, Issue 12, pages 1798–1804, August 13, 2012 DOI: 10.1002/cbic.201200187

Characterization of the Suillus grevillei Quinone Synthetase GreA Supports a Nonribosomal Code for Aromatic a-Keto Acids

Barbara Wackler 1, Dr. Gerald Lackner 1, Dr. Yit Heng Chooi 1, 2, Prof. Dr. Dirk Hoffmeister 1
1Friedrich-Schiller-Universitat, Department Pharmaceutical Biology at the Hans-Knoll-Institut, Beutenbergstrasse 11a, 07745 Jena (Germany) 2Current Address: University of California, Los Angeles, Department of Chemical and Biomolecular Engineering, Los Angeles, CA 90095 (USA)

... The DNA sequence of the combined insert sequences of these cosmids has been deposited in GenBank (#JQ681152) and was submitted to FGENESH (Softberry, Mount Kisco, NY) and to the BLAST server,29 to identify genes and exon/intron junctions. ...


The Plant Journal
Volume 72, Issue 1, pages 142–153, October 2012 DOI: 10.1111/j.1365-313X.2012.05072.x

The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements

Staton et al.,
1 Department of Genetics, University of Georgia, Athens, GA 30602, USA 2 Division of Biology, 426 Ackert Hall, Kansas State University, Manhattan, KS 66506, USA

... The bias in the EST matches to Gypsy elements, and the biased genomic abundance of these sequences are shown in the tracks below the predicted genes. Gene predictions were made using fgenesh (http://www.softberry.com) and maker (http://gmod.org/wiki/MAKER). ...


Chemistry & Biology
Volume 19, Issue 12, 21 December 2012, Pages 1611–1619 DOI: 10.1016/j.chembiol.2012.10.010

Terpendole E, a Kinesin Eg5 Inhibitor, Is a Key Biosynthetic Intermediate of Indole-Diterpenes in the Producing Fungus Chaunopycnis alba

Takayuki Motoyama1, Toshiaki Hayashi1, Hiroshi Hirota1, Masashi Ueki1, Hiroyuki Osada1
1 Chemical Biology Core Facility, Chemical Biology Department, RIKEN Advanced Science Institute, Wako-shi, Saitama 351-0198, Japan

... Nucleotide and amino acid sequence data were analyzed by DNASIS-Mac software (Hitachi Software Engineering, Tokyo, Japan). Open reading frames were predicted by FGENESH and FGENESH + software (Softberry, Mount Kiscko, NY). Construction of Recombinant Strains. ...


BMC Genomics
2012, 13:553 doi:10.1186/1471-2164-13-553

Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC

Biao Wang 1*, Robert Ekblom 2, Tanja M Strand 1,3, Silvia Portela-Bens 1 and Jacob Hoglund 1
1 Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, Uppsala, SE-752 36, Sweden 2 Evolutionary Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, Uppsala, SE-752 36, Sweden

... Identification of coding regions and putative exons was conducted by three different gene prediction programs: Fgenesh ( http://www.softberry.com webcite), GeneMark.hmm ( http://exon.gatech.edu webcite) and Genscan ( http://genes.mit.edu/GENSCAN.html webcite) [ ...


PNAS
August 21, 2012 vol. 109 no. 34 13716-13721 DOI: 10.1073/pnas.1121096109

Rapid divergence and expansion of the X chromosome in papaya

Gschwend et al.,
aDepartment of Plant Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; bTexas AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A & M University, Weslaco, TX 78596;

... V. monoica Gene Prediction. Genes were predicted in the V. monoica BACs using Genscan (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://linux1.softberry.com/berry.phtml), as well as homology to papaya-expressed sequence tags (ESTs) and gene models. ...


Theoretical and Applied Genetics
Volume 125, Issue 2 , pp 273-284 DOI: 10.1007/s00122-012-1832-8

Fine mapping of fw3.2 controlling fruit weight in tomato

Na Zhang, Marin Talbot Brewer, Esther van der Knaap
1. Department of Horticulture and Crop Science, The Ohio State University/OARDC, 217A Williams Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA 2. Department of Plant Pathology, University of Georgia, Athens, GA, USA

... The sequence of the BAC C03Hba0051C24 encompassing fw3.2 was analyzed with the ab initio gene prediction pro- grams FGENESH (http://www.softberry.com/berry.phtml) (Salamov and Solovyev 2000) and is consistent with the recently released annotation of the tomato ...


BMC Genomics
2012, 13:444 http://www.biomedcentral.com/1471-2164/13/444 doi:10.1186/1471-2164-13-444

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Suzuki et al.,
1 Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada

...Using the repeat-masked assembly, several gene prediction programs falling into three general categories were used: 1) ab initio - FGENESH [52]; GeneMark [53], 2) homology-based - FGENESH+; Genewise [54] seeded by BLASTx alignments against GenBank’s database of non-redundant proteins (NR: [55]), and 3) EST-based - EST_map [56] seeded by EST contigs....


BMC Genomics
2012, 13:270 http://www.biomedcentral.com/1471-2164/13/270 doi:10.1186/1471-2164-13-270

The WRKY transcription factor family in Brachypodium distachyon

Tripathi et al.,
1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA

... Each potential gene was then manually curated using both FGENESH [38] and...


PLoS ONE
7(3): e32658. doi:10.1371/journal.pone.0032658

Membrane Topology and Predicted RNA-Binding Function of the ‘Early Responsive to Dehydration (ERD4)’ Plant Protein

Archana Rai, Penna Suprasanna, Stanislaus F. D'Souza, Vinay Kumar
Nuclear Agricultural & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India

...Gene structure study was performed using popular gene finding pipeline (FGENESH at www.softberry.com)...


BMC Genomics
2012, 13:171 doi:10.1186/1471-2164-13-171

Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer

Hu et al.,
1 Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA 2 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA

... Gene prediction, codon usage analysis & repetitive DNA identification. Gene prediction was conducted using FGENESH [47], an ab initio gene predictor provided in the Softberry website. A pre-trained Alternaria matrix was used to optimize predictions. ...


BMC Genomics
2012, 13:674 doi:10.1186/1471-2164-13-674

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

Martin et al.,
1 Philip Morris International R&D, Philip Morris Products SA, Neuchatel 2000, Switzerland 2 Institut fur Mathematik und Informatik, Greifswald D-17487, Germany

...FGENESH was trained for tobacco by SoftBerry Inc. and run as an ab initio gene finder with default parameters. Further iterations of the tobacco genome assembly were also ...


The Plant Journal
Volume 72, Issue 2, pages 212–221, October 2012 DOI: 10.1111/j.1365-313X.2012.05059.x

Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses

Qinghua Wang 1, Hugo K. Dooner 1,2
1 Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA 2 Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA

... The Fgenesh gene prediction program (http://www.softberry.com) was used to annotate the non-orthologous genes in Coix and sorghum, and adjustment of exon/intron structures was based on the sorghum and rice transcript annotation. ...


Plant Physiology
July 2012 vol. 159 no. 3 1086-1098 doi: http://dx.doi.org/10.1104/pp.112.197483

Altered Chloroplast Development and Delayed Fruit Ripening Caused by Mutations in a Zinc Metalloprotease at the lutescent2 Locus of Tomato

Barry et al.,
Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 (C.S.B., Q.M.) Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (G.M.A., R.P.M., J.J.G.)

...The prediction of genes within genomic DNA sequence was performed using the FGENESH hidden Markov model-based gene structure prediction program (http://linux1.softberry.com/berry.phtml). ...


Front Plant Sci.
2012; 3: 5. DOI: 10.3389/fpls.2012.00005

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

Leroy et al.,
1 UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche Agronomique-Universite Blaise Pascal, Clermont-Ferrand, France 2 National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan

For ab initio gene prediction, TriAnnot uses four programs: FGeneSH [17], GeneID (Guigo et al., 1992), GeneMarkHMM


BMC Plant Biology
2012, 12:20 doi:10.1186/1471-2229-12-20

Comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self-incompatibility response of Citrus clementina

Caruso et al.,
1 Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Universita degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy 2 Institut Valencia d'Investigacions Agraries - Centre de Genomica, Carretera Montcada de l'Horta-Naquera Km. 4,5, 46113 Montcada de l'Horta (Valencia), Spain

...ORF prediction was based on the genome browser data for each analyzed species as well as Fgenesh analysis http://www.softberry.com...


PLoS ONE
7(2): e32010. doi:10.1371/journal.pone.0032010

A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

Gao D, Chen J, Chen M, Meyers BC, Jackson S
Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

...To predict the sequences in sorghum and maize, 20 kb of flanking sequence (10 kb on each side of the transposon) were analyzed by the FGENESH (http://linux1.softberry.com) and the GeneMark.hmm ...


PLoS Pathog
8(9): e1002952. doi:10.1371/journal.ppat.1002952

Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

Gardiner DM et al.,
Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland, Australia Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland

...Protein coding genes were ab initio predicted in the F. pseudograminearum genome using FGENESH [52] based on the F. graminearum gene models as part of the MolQuest2 package from Softberry, AUGUSTUS [53] and GeneMark-ES...


PLoS ONE
7(2): e31149. doi:10.1371/journal.pone.0031149

Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

Hu et al.,
CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China

... For the misannotated genes, manual reannotation was performed using online web server FGENESH (http://linux1.softberry.com/berry.phtml). ...


Theoretical and Applied Genetics
Volume 125, Issue 5 , pp 1047-1055 DOI 10.1007/s00122-012-1894-7

The isolation of Pi1, an allele at the Pik locus which confers broad spectrum resistance to rice blast

Lixia Hua et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropic Agrobioresources, Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China 2. National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan

... The gene annotation tools RiceGAAS (http://ricegaas.dna.affrc. go.jp) and FGENESH (http://www.softberry.com) were then used to identify Pi1 candidates within the 277-kb segment of cv. Nipponbare defined by the closest flanking markers (CRG11-7 and K28). ...


Bioresource Technology
Volume 121, October 2012, Pages 404–410 http://dx.doi.org/10.1016/j.biortech.2012.07.027

Two neutral thermostable cellulases from Phialophora sp. G5 act synergistically in the hydrolysis of filter paper

Junqi Zhao et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China

... Transcription initiation sites and intron and exon information were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The presence of signal peptides was predicted using SignalP 4.0 (http://www.cbs.dtu.dk/services/SignalP/). ...


Theoretical and Applied Genetics
Volume 125, Issue 4 , pp 773-779 DOI 10.1007/s00122-012-1870-2

Fine mapping and candidate gene analysis of the nuclear restorer gene Rfp for pol CMS in rapeseed (Brassica napus L.)

Zhi Liu et al.,
1. National Key Lab of Crop Genetic Improvement, National Center of Rapeseed Improvement (Wuhan Branch), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

... Candidate gene identification and sequence analysis The online system FGENESH (http://www.softberry.com) was used to identify predicted ORFs in the delimited gene region. ... b Candidate region of the Rfp locus and the predicted gene from http://www.softberry. com. ...


Plant Molecular Biology Reporter
Volume 30, Issue 4 , pp 1025-1031 DOI 10.1007/s11105-011-0408-0

Identification and Association Analysis of Castor Bean Orthologous Candidate Gene-Based Markers for High Oil Content in Jatropha curcas

Arti Sharma (1) Rajinder Singh Chauhan (1)
1. Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan, 173 215, HP, India

... gene sequences from other plants (Arabidopsis, Brassica, Medicago, sunflower, soybean, and cotton) were downloaded and annotated for open reading frames, including the 5? and 3?UTRs using gene prediction algorithms of FGenesH (http://sun1.softberry.com/berry. ...


The Journal of Biological Chemistry
doi: 10.1074/jbc.M111.317982 January 6, 2012, 287, 1371-1380.

Biochemical Characterization of Indole Prenyltransferases FILLING THE LAST GAP OF PRENYLATION POSITIONS BY A 5-DIMETHYLALLYLTRYPTOPHAN SYNTHASE FROM ASPERGILLUS CLAVATUS

Xia Yu ‡,1, Yan Liu ‡§,2, Xiulan Xie ¶, Xiao-Dong Zheng § and Shu-Ming Li ‡,3
From the ‡Institut fur Pharmazeutische Biologie und Biotechnologie, Philipps-Universitat Marburg, Deutschhausstrasse 17A, 35037 Marburg, Germany, the §Department of Food Science and Nutrition, Zhejiang University, 310058 Hangzhou, Zhejiang, China, and the ¶Fachbereich Chemie, Philipps-Universitat Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany

... gov). FGENESH from Softberry and the DNASIS software package (version 2.1, Hitachi Software Engineering, San Bruno, CA) were used for exon prediction and sequence analysis, respectively. Chemicals. Dimethylallyl diphosphate ...


Functional & Integrative Genomics
Volume 12, Issue 3 , pp 489-500 DOI 10.1007/s10142-012-0283-2

New cis-regulatory elements in the Rht-D1b locus region of wheat

Jialei Duan et al.,
1. College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, 100094, Beijing, People’s Republic of China

... usda.gov/ITMI/Repeats/gene_annotation.pdf). Gene pre- dictions were accomplished mainly by using the program FGENESH with the monocot (corn, rice, wheat, and barley) training set (http://www.softberry.com). GENSCANW ...


Molecules and Cells
Volume 33, Issue 4 , pp 415-422 DOI 10.1007/s10059-012-0017-2

Ectopic expression of Capsicum-specific cell wall protein Capsicum annuum senescence-delaying 1 (CaSD1) delays senescence and induces trichome formation in Nicotiana benthamiana

Eunyoung Seo et al.,
2. Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea 1. Seeders Inc., Daejeon, 305-509, Korea

... an- nuum 'CM334' (Yoo et al., 2003). Both the gene-coding region and the 3? untranslated region were predicted using the FGENESH program (http://linux1. softberry.com/berry.phtml). Gene-specific primers were designed for ...


Mol Biol Evol
(2012) 29 (1): 91-100. doi: 10.1093/molbev/msr149

Ancestral Ca2+ Signaling Machinery in Early Animal and Fungal Evolution

Xinjiang Cai *,1 and David E. Clapham * 2,3
1Molecular Pathogenesis Program, The Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center 2Howard Hughes Medical Institute, Department of Cardiology, Children's Hospital Boston 3Department of Neurobiology, Harvard Medical School

... 2005) and FGENESH programs (http://www.softberry.com/berry.phtml?topic=index&group= programs&subgroup=gfind) were used to predict the genes of interest by using identified DNA segments and their neighboring regions of genomic sequences. ...


POJ
5(2):94-102 (2012)

Genome-wide analysis of cytosolic and chloroplastic isoforms of glutathione reductase in plant cells

Ahmad Tahmasebi 1, Farzaneh Aram 2, Mansour Ebrahimi 3, Manijeh Mohammadi-Dehcheshmeh 4, Esmaeil Ebrahimie 1&5*
1Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran 2Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz University, Shiraz, Iran

...Genomic sequences were also analyzed in the FGENESH gene structure prediction program (http://www.softberry.com) and GeneMark program (http://opal.biology.gatech.edu/GeneMark).... ...Protein sorting and subcellular localization predictions were performed according to ProtComp program Version 5 (http://www.softberry.com/)...


Phytopathology
May 2012, Volume 102, Number 5 Pages 506-518 http://dx.doi.org/10.1094/PHYTO-06-11-0180

Evidence for Morphological, Vegetative, Genetic, and Mating-Type Diversity in Sclerotinia homoeocarpa

Daniele Liberti, Jeffrey A. Rollins, and Philip F. Harmon
Department of Plant Pathology, 1453 Fifield Hall, University of Florida, Gainesville 32611.

... analysis. Protein prediction analysis was performed using ab initio gene prediction software FGENESH (36) running on the Softberry web interface (http:// www.softberry.com) selecting S. sclerotiorum as the reference ge- nome. ...


Phytopathology
February 2012, Volume 102, Number 2 Pages 222-228 http://dx.doi.org/10.1094/PHYTO-03-11-0075

Identification and Fine-Mapping of Xa33, a Novel Gene for Resistance to Xanthomonas oryzae pv. oryzae

P. Natraj Kumar et al.,
Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, India.

... Identification of putative candidate genes. The genomic se- quence between the flanking SSR markers was downloaded from Japonica rice genome and analyzed using the online software FGENESH (http://www.softberry.com). ... softberry.com). ...


Plant and Soil
July 2012, DOI 10.1007/s11104-012-1345-x

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

M. Migocka, A. Warzybok, G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland

... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was determined using FGENESH or FGENESH+ programs available on softberry.com ...


Molecular Genetics and Genomics
Volume 287, Issue 4 , pp 295-311 DOI 10.1007/s00438-012-0675-y

Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a model

Jian Wu et al.,
1. Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, 310058, Hangzhou, People’s Republic of China

... After searching for IAA genes, bioinformatics tools, such as DNASTAR and FGENESH (http://linux1.softberry.com/berry) were used to analyze and predict those unknown IAAs. Isolation of the open reading frame (ORF) cDNA sequences ...


Gene
Volume 499, Issue 1, 10 May 2012, Pages 108–120 http://dx.doi.org/10.1016/j.gene.2012.01.048

Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum

Fuling Kong et al.,
Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou 310058, People's Republic of China

... After searching for MAPK gene family, DNASTAR and FGENESH (http://linux1.softberry.com/berry) were used to analyze and predict those MAPK domains. ... Each predicted SlMAPK sequence was confirmed by FGENESH (http://www.softberry.com/berry.phtml?topic=fgenesh). ...


Journal of Integrative Plant Biology
Volume 54, Issue 5, pages 321–329, May 2012 DOI: 10.1111/j.1744-7909.2012.01112.x

Identification and Fine Mapping of rhm1 Locus for Resistance to Southern Corn Leaf Blight in Maize

Yuanzeng Zhao et al.,
1 State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China 2 Department of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China

... region contains only one putative protein-coding gene using the FGENESH gene prediction program (http://linux1.softberry.com/berry.phtml). This predicted gene was a homologue of ... monocot training set (http://linux1.softberry.com/berry.phtml). The predicted genes were ...


Theoretical and Applied Genetics
September 2012 DOI 10.1007/s00122-012-1975-7

Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.)

D. Huang et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Agricultural College, Guangxi University, Nanning, 530005, China 2. Rice Research Institute, Plant Protection Institute and Guangxi Rice Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China

... The putative open reading frame (ORF) in the target region was predicted by the online software GENESCAN and FGENESH of Softberry (www.softberry.com/berry.phtml) with monocot plants as the model organism. Host selection behavior ...


Gene
Volume 507, Issue 1, 1 October 2012, Pages 54–60 http://dx.doi.org/10.1016/j.gene.2012.07.004,

Characterization of Aquilegia Polycomb Repressive Complex 2 homologs reveals absence of imprinting

Emily J. Gleason a, b, Elena M. Kramer a,
a Dept. of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave. Cambridge, MA, 02138, USA b Dept. of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave. Cambridge, MA, 02138, USA

... the query sequence. We then used the SoftBerry FGENESH program (http://linux1. softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) to predict open reading frames for the loci. cDNA sequences were ...


African Journal of Biotechnology
Vol. 11(40), pp. 9534-9542, 17 May, 2012 DOI: 10.5897/AJB12.040

Isolation and characterization of a candidate gene for resistance to cereal cyst nematode from Aegilops variabilis in China

D. L. Xu et al.,
1 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China. 2 Graduate University of the Chinese Academy of Sciences, Beijing, China.

... The ORFs of the sequences were identified by FGENESH (http://linux1.softberry.com/) and the amino acid sequence was obtained at the same time. ... The resulting sequences were analyzed using NSITE-PL to identify regulatory motifs (http://linux1.softberry.com/). RESULTS ...


Theoretical and Applied Genetics
Volume 125, Issue 6 , pp 1125-1135 DOI 10.1007/s00122-012-1899-2

Characterization, fine mapping and expression profiling of Ragged leaves1 in maize

Haiying Guan et al.,
1. Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China 2. Department of Life Science and Technology, Henan Institute of Science and Technology, XinXiang, 453003, China

... 2004). The gene prediction was conducted by Softberry (http://linux1.softberry.com/berry. phtml?topic=fgenesh&group=programs&subgroup=gfind). Transcriptome sequencing and gene annotation The BC3 segregating population was grown in a green- house. ...


Molecular Genetics and Genomics
Volume 287, Issue 3 , pp 247-259 DOI 10.1007/s00438-012-0674-z

Candidate genes within a 143 kb region of the flower sex locus in Vitis

Iris Fechter et al.,
1. Julius Kuhn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833, Siebeldingen, Germany 2. Center for Biotechnology, Bielefeld University, 33594, Bielefeld, Germany

... PCR amplifications were per- formed to ensure order of contigs in cases of uncertainties. Gene prediction The sequences were annotated from the scaffolds using the software FGENESH (http://linux1.softberry.com/berry. phtml). ...


Braz. J. Plant Physiol.,
24(1): 69-73, 2012

Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings

Kalika Kuhar 1 , Varun Kumar Gupta 1 , Rekha Kansal 2 , Vijay Kumar Gupta 1 *
1 Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India. 2 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (PUSA), New Delhi, India.

... The nucleotide sequence was analyzed in silico using VecScreen program of National Center for Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST), FGENESH program of Softberry web server and BioEdit. ...


Mol Biol Evol
2012, 29 (2): 631-645. doi: 10.1093/molbev/msr208

Zisupton—A Novel Superfamily of DNA Transposable Elements Recently Active in Fish

Astrid Bohne et al.,
1Institut de Genomique Fonctionnelle de Lyon, Universite de Lyon, Universite Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Superieure de Lyon, Lyon, France 2Department of Physiological Chemistry I, Biocenter, University of Wurzburg, Wurzburg, Germany

... 10 ?05 . Automatic sequence annotation was refined manually using expressed sequence tag data and related protein sequences with the help of FGENESH on the softberry web server (http://linux1.softberry.com). Nucleotide ...


3 Biotech.
2012 September; 2(3): 199–209. Published online 2012 March 24. doi: 10.1007/s13205-012-0047-7

Cloning, characterization and expression analysis of a novel gene encoding Kunitz-type protease inhibitor from Dolichos biflorus

Kalika Kuhar,1 Rekha Kansal,2 Amit Mishra,2 Kirpa Ram Koundal,2 and Vijay Kumar Gupta 1
1Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana India 2National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (PUSA), New Delhi, India

... The primers were designed from the coding region of the genes determined through Softberry software following the standard rules and analyzed using Fast PCR software for self-dimers, melting temperature ... 2) as predicted by FGENESH program of Softberry web server. ...


FGENESH 2011

Immunogenetics
2011 Nov;63(11):753-71. doi: 10.1007/s00251-011-0549-1. Epub 2011 Jun 28.

Defining the turkey MHC: identification of expressed class I- and class IIB-like genes independent of the MHC-B

Reed et al.,
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA

... Final assembly of repeated contigs was confirmed by PCR and resequencing. Gene identification and annotation Sequences were analyzed with Softberry FGENESH and BLAST (http://linux1.softberry.com/all.htm) to identify putative transcripts and homologies to known genes. ...


Journal of Insect Physiology
Volume 58, Issue 4, April 2012, Pages 570–579 DOI: 10.1016/j.jinsphys.2011.12.009

Localization of two Na+- or K+-H+ antiporters, AgNHA1 and AgNHA2, in Anopheles gambiae larval Malpighian tubules and the functional expression of AgNHA2 in yeast

Minghui A. Xiang a, c, Paul J. Linser b, David A. Price b, William R. Harvey b, c, d, e
a Division of Nephrology and Hypertension, Department of Medicine, University of Florida-Jacksonville, Jacksonville, FL 32206, USA b Whitney Mosquito Biology Group, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA

... gambiae that were applied to FGENESH at the Softberry site (http://www.softberry.com/berry.phtml) identified a cDNA from a genomic region of 30 kb; it included the originally predicted cDNA exons and predicted two more exons at the 5? end although it had the same 3 ...


BMC Proceedings
2011, 5(Suppl 7):P65 doi:10.1186/1753-6561-5-S7-P65

Genome characterization of a Eucalyptus natural mutant

Fuchs et al.,
1 Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubiao Jr s/n CEP 18618-000, Botucatu (SP), Brazil 2 Departamento de Genetica, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de Sao Paulo (USP), Avenida Padua Dias, 11 CEP 13418-900, Piracicaba (SP), Brazil

... phytozome.net/ webcite) using BLAST. The genomic region identified was analyzed by FGENESH tool (Softberry, Inc. – http://www.softberry.com webcite) to find predicted genes in the region. Predicted genes were translated ...


Journal of Insect Physiology
Volume 57, Issue 9, September 2011, Pages 1190–1197 DOI: 10.1016/j.jinsphys.2011.05.011

Functions of duplicated genes encoding CCAP receptors in the red flour beetle, Tribolium castaneum

Bin Li a, 1, Richard W. Beeman b, Yoonseong Park a
a Department of Entomology, Waters Hall, Kansas State University, Manhattan, KS 66506, USA b USDA-ARS Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS 66502, USA

... Initial search results were further analyzed using the gene prediction software FGENESH (http://linux1.softberry.com/berry.phtml). Similar methods were used to mine candidate CCAP receptors from other insect genomes for comparisons of gene structures and sequences. ...


Funct Integr Genomics.
2011 Dec;11(4):599-609. doi: 10.1007/s10142-011-0237-0. Epub 2011 Jul 16.

Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage

Zhang J, Jia J, Breen J, Kong X.
Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Science, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, People's Republic of China

... plot analysis (Krumsiek et al. 2007). Gene prediction and function assignment Gene prediction was performed using FGENESH at softberry web site (http://www.softberry. com) and GENES- CAN. Then, BLASTP against the non ...


Fungal Biology
Volume 116, Issue 2, February 2012, Pages 225–233 DOI: 10.1016/j.funbio.2011.11.005

mrflbA, encoding a putative FlbA, is involved in aerial hyphal development and secondary metabolite production in Monascus ruber M-7

Yishan Yang c, Li Li c, Xin Li c, Yanchun Shao a, c, Fusheng Chen a, b, c,
a State Key Laboratory of Agricultural Microbiology, Wuhan 430070, Hubei Province, PR China b Key Laboratory of Food Safety Evaluation of the Ministry of Agriculture, Wuhan 430070, Hubei Province, PR China

... Specific primers for 3'RACE were designed according to the predicted cDNA sequence of the mrflbA or mga1 gene using SoftBerry's FGENESH program (http://linuxl.softberry.com/ berry.phtml), while primers for 5'RACE were designed according to the sequences obtained by 3 ...


Breast Cancer Research and Treatment
Volume 130, Issue 3 , pp 1003-1010 DOI: 10.1007/s10549-011-1677-x

Further evidence for the contribution of the RAD51C gene in hereditary breast and ovarian cancer susceptibility

Vuorela et al.,
1. Laboratory of Cancer Genetics, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu University Hospital, P.O. Box 5000, 90014, Oulu, Finland 2. Department of Pathology and Forensic Medicine, School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, 70211, Kuopio, Finland

... 2). According to FPROM human promoter prediction software (Softberry, Inc., Mt. ... FGENESH (Softberry, Inc., Mt. Kisco, NY), are abolished. Based on bioinformatics, the observed 27 bp deletion thus produces a null allele, and is pathogenic. ...


Biologia Plantarum
Volume 55, Issue 4 , pp 614-624 DOI: 10.1007/s10535-011-0159-7

Molecular cloning and phylogenetic analysis of cereal type II metacaspase cDNA from wheat

E. Piszczek, M. Dudkiewicz, M. Sobczak
1. Department of Biochemistry, Warsaw University of Life Sciences, 159 Nowoursynowska, PL-02776, Warsaw, Poland 2. Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, 159 Nowoursynowska, PL-02776, Warsaw, Poland

... The identification of the coding region, open reading frame and the translation of TaeMCAII nucleotide sequence were made based on the FGENESH gene structure prediction using an HMM model constructed for monocot plants (SoftBerry software http://linux1.softberry.com ...


Plant Cell Reports
Volume 30, Issue 11 , pp 2059-2073 DOI: 10.1007/s00299-011-1113-z

Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum

J. Wu et al.,
1. Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Hangzhou, 310058, People’s Republic of China 2. Department of Horticulture, Zhejiang University, Hangzhou, 310058, People’s Republic of China

... databases. After searching for ARF genes, bioinformatics tools, such as DNASTAR and FGENESH (http://linux1.softberry.com/berry) were used to analyze and predict those unknown SlARFs. ... www. softberry.com/berry.phtml?topic=fgenesh). ...


Sains Malaysiana
40 (4). pp. 331-337. ISSN 0126-6039

Cloning and analysis of pyrG gene encoding orotidine 5-Monophosphate decarboxylase of aspergillus oryzaeStrain S1

Selina Oh Siew Ling, and Leong , Jiun Min and Abdul Munir Abdul Murad, and Nor Muhammad Mahadi , and Farah Diba Abu Bakar
BGI

... 475 bp). The pyrG contained one intron at position 623-687 bp based on the AUGUSTUS and FGENESH (SoftBerry) analysis corresponding to the intron present in the pyrG of A. oryzae (Accession Number: Y13811). In silico ...


Nucl. Acids Res.
(2011) 39 (suppl 1): D637-D639. doi: 10.1093/nar/gkq1016

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

Wong et al.,
1Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D-85764 Neuherberg, 2Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg

... Based on this set, all gene loci in FGDB v3.1 were re-annotated using a pipeline including (i) Fgenesh with different matrices (www.softberry.com); (ii) GeneMark-ES (8); (iii) Augustus with ESTs, precedingly annotated Fusarium models and/or Neurospora crassa protein ...


Theoretical and Applied Genetics
Volume 123, Issue 4 , pp 625-633 DOI: 10.1007/s00122-011-1612-x

Fine-mapping of the woolly gene controlling multicellular trichome formation and embryonic development in tomato

Changxian Yang, Hanxia Li, Junhong Zhang, Taotao Wang, Zhibiao Ye
1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China 2. Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China

... Protein coding genes were predicted from the resul- tant contig using the FGENESH program (http://linux1.soft- berry.com/berry.phtml). ... Analysis of the »200 kb sequence revealed that this fragment contains 19 ORFs as automatically predicted by FGENESH (http://softberry. ...


POJ
4(5):239-249(2011)

Comparative analysis of the genomic regions flanking Xa21 locus in indica and japonica ssp. of rice (Oryza sativa L.)

Kumar et al.,
1Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli Prof. C.R. Rao Road , Hyderabad 500046, India 2Department of Plant Pathology, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India

... Protcomp V 8.0 (http://linux1.softberry.com/ berry.phtml) analysis for the sub cellular location of proteins showed that 80% of the predicted TEs were nuclear in localization while the remaining were cytoplasmic or mitochondrial in both the rice lines (Table 9). GC Content in the ... ...Gene prediction from the 100 kb region flanking to Xa21 locus of chromosome 11 in japonica and indica rice was carried out using HMM based gene structure prediction software FGENESH tool (www.softberry.com) trained for monocot plant species (Salamov and Solovyer, 2000) ...


Eukaryotic Cell
doi: 10.1128/EC.05255-11 December 2011 vol. 10 no. 12 1740-1741

Draft Genome Sequence of Penicillium marneffei Strain PM1

Woo et al.,
1Department of Microbiology 2State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong

... genome, were sequenced. The Phred/Phrap/Consed software package was used for base calling and sequence assembly (1,–,5). Protein-coding genes and introns were predicted using FGENESH (Softberry). The draft genome ...


Theoretical and Applied Genetics
Volume 122, Issue 5 , pp 1017-1028 DOI: 10.1007/s00122-010-1506-3

The Pik-p resistance to Magnaporthe oryzae in rice is mediated by a pair of closely linked CC-NBS-LRR genes

Yuan et al.,
1. Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China 2. Hubei Academy of Agricultural Science, Wuhan, 430064, China

... Wang et al. 2009). The gene content in the equivalent interval of cv. Nipponbare was predicted using GENESCAN (http://genes.mit.edu/ GENSCAN.html) and FGENESH (http://www.softberry. com). DNA sequence comparisons ...


BMC Proceedings
2011, 5(Suppl 7):O17 doi:10.1186/1753-6561-5-S7-O17

High-throughput targeted SNP discovery using Next Generation Sequencing (NGS) in few selected candidate genes in Eucalyptus camaldulensis

Prasad S Hendre *, Rathinam Kamalakannan, Rathinavelu Rajkumar and Mohan Varghese
ITC R&D Centre, Peenya Insdustrial Area, No.3, 1st Main, 1st Phase, Bangalore- 560 058, Karnataka, India

... block. Web-based gene prediction tool FGENESH (http://linux1.softberry.com webcite) was used for identifying genic regions such as UTRs, exons and introns with Arabidopsis thaliana gene model. Results and discussion. Forty ...


Fungal Biology
Volume 115, Issue 8, August 2011, Pages 775–781 DOI: 10.1016/j.funbio.2011.06.002,

Characterisation of the ArmA adenylation domain implies a more diverse secondary metabolism in the genus Armillaria

Mathias Misiek, Jana Braesel, Dirk Hoffmeister
Friedrich-Schiller-Universitat Jena, Department Pharmaceutical Biology at the Hans-Knoll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany

... The Aspergillus, Laccaria, or Phanerochaete search algorithms of FGENESH (Softberry, Mount Kisco, NY) were used to predict gene structures and exon/intron junctions in the insert sequences of three previously identified Armillaria cosmids 108, 138, and 152 (Misiek & ...


Mol Biol Evol
(2011) 28 (6): 1913-1926. doi: 10.1093/molbev/msr012

Molecular Evolution of the Metazoan PHD–HIF Oxygen-Sensing System

Kalle T. Rytkonen *,1, Tom A. Williams 2, Gillian M. Renshaw 3, Craig R. Primmer 1 and Mikko Nikinmaa 1
1Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland 2Department of Genetics, University of Dublin, Trinity College, Dublin, Ireland

... surrounding the primary BlastP hits in the genome contigs and repredicted the gene structure using three independent pieces of software: GENESCAN (http://genes.mit.edu/GENSCAN.html), Augustus (http://augustus.gobics.de/), and FGENESH (http://linux1.softberry.com). ...


Theoretical and Applied Genetics
Volume 123, Issue 4 , pp 585-601 DOI: 10.1007/s00122-011-1609-5

Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry

Graham et al.,
1. Genetics Department, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK 2. Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, Scotland, UK

... Gene prediction Open reading frames from both BAC sequences were identified using the Softberry gene structure prediction program FGENESH (http://linux1. softberry.com/berry. phtml) using Vitis vinifera as the reference. ...


Applied Microbiology and Biotechnology
Volume 89, Issue 6 , pp 1851-1858 DOI: 10.1007/s00253-010-3016-2

An acid and highly thermostable xylanase from Phialophora sp. G5

Zhang et al.,
1. Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, China 2. School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, 430023, China

... ncbi.him.nih.gov/gorf/gorf/gorf.html). Genes, introns, exons and transcription initiation sites were predicted using the online software FGENESH (http://linux1.softberry.com/ berry.phtml). The signal peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184–194 DOI: 10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

Tiago M. Martins a, b, , , Virgilio E. do Rosario b, Ana Domingos a, b
a Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E ? 1e-04 was adopted for the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with multiple exons was predicted using the FGENESH and FGENESH+ software (http://www.softberry.com). ...


Advanced Studies in Biology
Vol. 3, 2011, no. 4, 169 – 180

Genetic Disease Resistance and Conservation of a Plant Gene that Encodes a Mitogen-Activated Protein Kinase Kinase Kinase

L. David Kuykendall, Jonathan Y. Shao, Rachel P. Naegele and J. Mitchell McGrath
Molecular Plant Pathology Laboratory, Plant Sciences Institute Beltsville Agricultural Research Center, Beltsville MD 20705, USA Department of Crop and Soil Sciences and USDA-ARS Sugar Beet and Bean Research, Michigan State University East Lansing, MI 48824-1325,USA

...The sequence contig was screened for coding sequence using a combination of the following programs: GeneMark [21] for eukaryotes:(http://exon.gatech.edu/GeneMark/eukhmm.cgi), GenScan [22] (http://genes.mit.edu/GENSCAN.html) FGENESH (http://linux1.softberry.com/berry.phtml...


Comparative and Functional Genomics
Volume 2011 (2011), Article ID 286089, 9 pages doi:10.1155/2011/286089

Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis in Jatropha curcas

Arti Sharma and Rajinder Singh Chauhan
Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan 173 215, India

... Castor bean genome sequence contigs harboring SSRs were annotated for putative open reading frames, including 5?UTRs and 3?UTRs, using gene prediction algorithms of FGenesH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind ...


Advanced Science Letters
Volume 4, Numbers 11-12, November 2011 , pp. 3653-3657(5) DOI: http://dx.doi.org/10.1166/asl.2011.2027

Cloning and Sequence Analysis of Candidate Disease Resistance Genes from Dongxiang Common Wild Rice (O. rufipogon Griff.)

Han, Xiaoxia et al.,
BGI

... The Genomic DNA Sequence Analysis DNA sequence location and similarity analysis was performed by BLAST program (http://www.ncbi.nlm.nih.gov/).13 Gene pre- diction was performed by FGENESH (Solovyev and Salamov 1999; http://www.softberry.com/berry.phtml) and ...


New Phytologist
2011, 192: 164–178. doi: 10.1111/j.1469-8137.2011.03800.x

Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny.

Ratnaparkhe et al.,
1 Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA 2 Center for Genomics and Computational Biology, School of Life Sciences, School of Sciences, Hebei United University, Tangshan, Hebei 063000, China

... sequenced. Assembled sequences were visualized and manually edited using Consed (Gordon et al., 1998). Peanut BAC sequences were annotated using gene prediction programs FGENESH (http://www.softberry.com). The ...


Plant Molecular Biology Reporter
Volume 29, Issue 4 , pp 769-783 DOI: 10.1007/s11105-010-0284-z

Genome-Wide Analysis of Fatty Acid Desaturases in Soybean (Glycine max)

Xiaoyuan Chi et al.,
1. Shandong Peanut Research Institute, Qingdao, 266100, People’s Republic of China 2. Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People’s Republic of China

... The searches were iterated until convergence. As for the incorrectly predicted genes, manual reannotation was performed using online web server FGENESH (http://linux1.softberry.com/berry.phtml; Salamov and Solovyev 2000). ...


Molecular Genetics and Genomics
Volume 285, Issue 1 , pp 79-90 DOI: 10.1007/s00438-010-0587-7

Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication

Xiaohui Zhang et al.,
1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China 2. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

... All new BLAST hits in the genomes, together with flanking regions of 5,000–10,000 bp at both sides, were annotated using the gene-finding programs FGENESH with the legume plant training set (http://www.softberry.com/) and GENSCAN with the Arabidopsis training set (http ...


Metabolic Engineering
Volume 13, Issue 6, November 2011, Pages 723–732 DOI: 10.1016/j.ymben.2011.09.008

Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1

Kangjian Qiao a, Yit-Heng Chooi a, Yi Tang a, b,
a Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States b Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States

... Gene predictions were performed via FGENESH program (www.softberry.com) and manually checked based on homologous gene/protein sequences in the GenBank database. Protein domain functions were deduced using Conserved Domain Search (NCBI). 2.3. ...


International Journal of Plant Genomics
Volume 2011 (2011), Article ID 370548, 8 pages doi:10.1155/2011/370548

Genes Encoding Callose Synthase and Phytochrome A Are Adjacent to a MAP3K?-Like Gene in Beta vulgaris US H20

L. David Kuykendall and Jonathan Y. Shao
Molecular Plant Pathology Laboratory, Agricultural Research Service, US Department of Agriculture, Plant Sciences Institute, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Building 004, Room 120, BARC-West, Beltsville, MD 20705, USA

... NCBI BLAST [8]. The 125 Kb sequence was screened for coding sequence using a combination of the following programs: GeneMark [9, 10] for eukaryotes (http://exon.gatech.edu/GeneMark/ eukhmm.cgi), Augustus (http://augustus.gobics.de/), and FgenesH (http://softberry.com ...


BMC Plant Biology
2011, 11:44 doi:10.1186/1471-2229-11-44

Characterisation of the legume SERK-NIK gene superfamily including splice variants: Implications for development and defence

Kim E Nolan, Sergey Kurdyukov and Ray J Rose
Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences. The University of Newcastle. University Dr. Callaghan, NSW, 2308, Australia

... potential coding regions from the individual genomic sequences were predicted using FGENESH software (Softberry; http://linux1.softberry.com webcite) ...


Journal of Bioscience and Bioengineering
Volume 112, Issue 6, December 2011, Pages 551–557 DOI: 10.1016/j.jbiosc.2011.08.018,

Acidic b-mannanase from Penicillium pinophilum C1: Cloning, characterization and assessment of its potential for animal feed application

Hongying Cai et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China 2 Department of Microbial Engineering, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China

... Introns, exons and transcription initiation sites were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). The signal peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). ...


Journal of Molecular Evolution
Volume 72, Issue 5-6 , pp 498-509 DOI: 10.1007/s00239-011-9448-1

Co-Variation Among Major Classes of LRR-Encoding Genes in Two Pairs of Plant Species

Jiao Wang, Shengjun Tan, Li Zhang, Ping Li, Dacheng Tian
1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China 2. Rice Research Institute, Sichuan Agricultural University, Wenjiang, 611130, China

.. Their sequences and corresponding annotations were downloaded from the online databases (Table S1). The annotation methods and quality could affect the gene identification. To estimate the bias, we used the ab initio gene finder FGENESH (http://linux1.softberry. ...


New Phytologist
189: 321–334. doi: 10.1111/j.1469-8137.2010.03462.x

The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication.

Zhai et al.,
1 Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China 2 Rice Research Institute, Guangdong Provincial Academy of Agricultural Sciences, Guangzhou, 510640, China

... Candidate gene identification. The gene annotation tools RiceGAAS (http://ricegaas.dna.affrc. go.jp) and FGENSH (http://www.softberry.com) were used to identify Pik candidates within the 166-kb segment of cv Nipponbare defined by the flanking markers K34 and K28 (Fig. 1a). ...


Process Biochemistry
Volume 46, Issue 12, December 2011, Pages 2341–2346 DOI: 10.1016/j.procbio.2011.09.018,

A novel thermoacidophilic family 10 xylanase from Penicillium pinophilum C1

Cai et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China

... The signal peptide was predicted using SignalP (http://www.cbs.dtu.dk/services/SignalP/). The exon–intron structure and transcription initiation sites of the full-length gene were predicted using the online software FGENESH (http://linux1.softberry.com/berry.phtml). ...


International Journal of Plant Genomics
Volume 2011 (2011), Article ID 291563, 12 pages doi:10.1155/2011/291563

Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5

Hiroshi Shinozuka, 1,2,3 Noel O. I. Cogan, 1,2,3 German C. Spangenberg, 1,2,3,4 and John W. Forster 1,2,3,4
1Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, VIC 3083, Australia 2Molecular Plant Breeding Cooperative Research Centre, Bundoora, VIC 3083, Australia

... Gene structure prediction was performed using the FGENESH program with the parameter setting for monocot plants (http://linux1.softberry.com/berry.phtml). Phylogenetic analysis was performed using the CLUSTALW program (http://www.genome.jp/tools/clustalw/). ...


Advanced Studies in Biology
Vol. 3, 2011, no. 1, 13 - 24

A Plant Gene Encodes a ‘HSFA9-like’ Heat Shock Factor and is Part of a Cluster of Orthologous Genes Including NPR1, CaMP and CK1 in Beta vulgaris, Populus trichocarpa, Solanum lycopersicum and Vitis vinifera

David Kuykendall, Jonathan Shao, Kate Burdekin and Lauren Conway
Molecular Plant Pathology Laboratory, PSI, BARC 10300 Baltimore Avenue, Beltsville, MD 20705 USA

...Putative genes in these genomic regions were annotated using FGenesH program (Gene finding in Eukaryota, http://linux1.softberry.com/). ...


The Journal of Microbiology
Volume 49, Issue 3 , pp 473-480 DOI: 10.1007/s12275-011-0362-4

Isolation and characterization of a reducing polyketide synthase gene from the lichen-forming fungus Usnea longissima

Wang et al.,
1. Korean Lichen Research Institute, Sunchon National University, Sunchon, 540-742, Republic of Korea

... The potential open reading frame (ORF) of FoNRks2662 was scanned with FGENESH (Berg et al., 2008) using Aspergillus as the matrix (http://linux1. softberry.com). The putative function of these ORFs was determined using a basic local alignment search tool (BLAST). ...


Genome
2011, 54(12): 1041-1044, DOI: 10.1139/g11-068

Isolation of a strawberry gene fragment encoding an actin depolymerizing factor-like protein from genotypes resistant to Colletotrichum acutatum

Marta Ontivero, a Gustavo Martinez Zamor a,b Sergio Salazar, c Juan Carlos Diaz Ricci, b Atilio Pedro Castagnaro a
Seccion Biotecnologia, Estacion Experimental Agroindustrial Obispo Colombres-Unidad Asociada al INSIBIO, Av. William Cross 3150, 4101 Las Talitas, Tucuman, Argentina. bInstituto Superior de Investigaciones Biologicas (INSIBIO; CONICET- UNT) and Instituto de Quimica Biologica “Dr. Bernabe Bloj”, Universidad Nacional de Tucuman. Chacabuco 461, 4000 Tucuman. Argentina.

... The deduced amino acid sequence showed identity scores ranging between 93% and 60%, with E values comprised between 1 ? 10 –37 and 6 ? 10 –44 . The gene prediction programs SPL and FGENESH 2.6 (www.softberry.com) (Solovyev et al. ...


Plant Molecular Biology
Volume 77, Issue 1-2 , pp 59-75 DOI: 10.1007/s11103-011-9794-9

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

Veronique Sarilar, Anne Marmagne, Philippe Brabant, Johann Joets, Karine Alix
1. AgroParisTech/CNRS, UMR 0320/UMR 8120 Genetique Vegetale INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France 2. CNRS, UMR 0320/UMR 8120 Genetique Vegetale INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France

... We used a combination of FGENESH v.2.6 (http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&subgroup=gfind, Salamov and Solovyev 2000), with arabidopsis thaliana (arabidopsis) as the reference model, and BLASTP to characterize the genomic ...


Front Plant Sci.
2011; 2: 35. DOI: 10.3389/fpls.2011.00035

Mining Disease-Resistance Genes in Roses: Functional and Molecular Characterization of the Rdr1 Locus

Terefe-Ayana et al.,
1Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany

... Gene prediction and annotation. Bioedit (Hall, 1999) was used for viewing and editing of sequences. Gene prediction and annotation was done using the gene prediction programs FGENESH and GENSCAN (http://www.softberry.com; http://genes.mit.edu/GENSCAN.html). ...


Journal of Plant Genetics and Transgenics
Vol 2, No 1 (2011) Chandel

In Silico Expression Analysis of QTL Specific Candidate Genes for Grain Micronutrient (Fe/Zn) Content Using ESTs and MPSS Signature Analysis in Rice (Oryza sativa L.)

Girish Chandel, P. Samuel, M. Dubey, R. Meena
BGI

... The nucleotide sequences were downloaded and analyzed for open reading frames (ORFs) and the CDS (Coding DNA sequence) using gene prediction algorithms of FGenesH (http://sun1.softberry.com/berry.phtml?topic=fgenesh&group =programs&subgroup=gfin). ...


Plant Physiology
March 2011 vol. 155 no. 3 1301-1311 DOI: 10.1104/pp.110.168500

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domesticationome

Zhu et al.,
National Center for Gene Research and Institute of Plant Physiology and Ecology (B.-F.Z., L.S., Y.Z., J.Z., Y.S., D.L., D.F., C.L., B.H.) and State Key Laboratory of Plant Molecular Genetics and Institute of Plant Physiology and Ecology (H.L.), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China;

... fully sequenced (Fig. 2C). Only one open reading frame (ORF) was identified in the 8.8-kb DNA fragment using FGENESH gene prediction analysis (http://linux1. softberry.com/berry.phtml; Fig. 2D). Two BACs corresponding ...


PLoS ONE
6(8): e24230. doi:10.1371/journal.pone.0024230

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

Cantu et al.,
Department of Plant Sciences, University of California Davis, Davis, California, United States of America Genome Center, University of California Davis, Davis, California, United States of America

... 12]. Exon-intron structures of transposable elements were predicted with the aid of Softberry FGENESH (linux1.softberry.com). Protein sequences of transposable elements were aligned using MAFFT with the linsi option [29]. ...


J. Exp. Bot.
(2011) 62 (8): 2585-2597. doi: 10.1093/jxb/erq433

Time course and amplitude of DNA methylation in the shoot apical meristem are critical points for bolting induction in sugar beet and bolting tolerance between genotypes

Trap-Gentil et al.,
1Universite d'Orleans, UFR-Faculte des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), rue de Chartres, BP 6759, F-45067 Orleans, France 2INRA, USC1328 Arbres et Reponses aux Contraintes Hydriques et Environnementales (ARCHE), F-45067 Orleans, France

... The determination of transposable elements (TEs) in the BvFLC and BvVIN3 genomic sequences was realized by the identification of potential coding sequences (Fgenesh on http://linux1.softberry. com/berry.phtml) followed by similarity analysis using BLASTP and analysis of ...


African Journal of Biotechnology
Vol. 10 (66), pp. 14738-14745, 26 October, 2011 DOI: 10.5897/AJB11.667

Isolation of candidate disease resistance genes from enrichment library of Oryza minuta based on conserved domains

Han et al.,
1State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410125, P. R. China. 2China National Hybrid R&D Center, Changsha 410125, P. R. China.

... The gene prediction program used was FGENESH (http:// www.softberry.com.cn), and the domains were predicted by the SMART program (http://smart.embl-heidelberg.de/) and CDD program (http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd). Results. ...


Molecular Breeding
Volume 28, Issue 3 , pp 343-357 DOI: 10.1007/s11032-010-9487-0

Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators

M. Migocka, A. Papierniak
1. Department of Plant Physiology, Institute of Plant Biology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland

... The selected cucumber sequences were then input into the programs identifying the full cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.gatech.edu/ eukhmm.cgi) and FGENESH (http://www.softberry.ru/berry.phtml). ...


BMC Evolutionary Biology
2011, 11:165 doi:10.1186/1471-2148-11-165

Immunoglobulin heavy chains in medaka (Oryzias latipes)

Susana Magadan-Mompo 1, Christian Sanchez-Espinel 2 and Francisco Gambon-Deza 3
1 Oceanographic Center of Vigo, Spanish Institute of Oceanography (IEO), Subida a Radio Faro 50, 36390 Vigo, Pontevedra, Spain 2 Shared Unit of Immunology, University of Vigo - Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As LagoasMarcosende, Vigo 36310, Pontevedra, Spain

... immunoglobulin mRNAs. Limits of unpublished antibodies were deduced following instructions in the software FGENESH (http://www.softberry.com webcite) and Augustus (http://augustus.gobics.de/submission webcite) [26]. Messenger ...


New Phytologist
189: 710–722. doi: 10.1111/j.1469-8137.2010.03492.x

Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum.

Rubini et al.,
1 National Research Council, Plant Genetics Institute – Perugia Division, Via della Madonna Alta 130, I–06128 Perugia, Italy 2 UMR 1136, Interactions Arbres/Microorganismes, INRA-Nancy, F–54280 Champenoux, France

... comparison and dotplot analysis were carried out using National Center for Biotechnology Information (NCBI) blast and Dotmatcher (EMBOSS Package v. 6.0.1). Gene structure prediction of MAT1-1-1 was performed with fgenesh software (http://linux1.softberry.com) using ...


Journal of Plant Biology
Volume 54, Issue 5 , pp 294-302 DOI: 10.1007/s12374-011-9166-7

Genetic Variation and Evolution of the Pi9 Blast Resistance Locus in the AA Genome Oryza Species

Liu et al.,
1. Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, Hunan, 410128, China 3. Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin, 446–701, South Korea

... by MEGA 4.0. Gene coding regions were predicted with GeneScan (http://genes.mit.edu/ GENSCAN.html) and Fegenesh (http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&subgroup=gfind) using the Pi9 sequence as the reference. ...


Molecular Genetics and Genomics
Volume 286, Issue 1 , pp 21-36 DOI: 10.1007/s00438-011-0616-1

Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition

Ulloa et al.,
1. USDA-ARS, Western Integrated Cropping Systems Research Unit, 17053 N. Shafter Ave., Shafter, CA, 93263, USA 2. Department of Nematology, University of California-Riverside, Riverside, CA, 92521, USA

... for analysis. Gene predic- tion and annotation were performed with the gene predic- tion programs Augustus (Stanke and Morgenstern 2005) and FGENESH (Softberry Mount Kisco, NY, USA, http:// www.softberry.com). Local ...


Journal of Industrial Microbiology & Biotechnology
Volume 38, Issue 9 , pp 1211-1218 DOI: 10.1007/s10295-010-0899-y

a-Amylase activity during pullulan production and ?-amylase gene analyses of Aureobasidium pullulans

Manitchotpisit et al.,
1. Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand 2. Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand

... CA). The mRNA sequence, amino acid sequence, initial start codon, stop codon, and number of exons were predicted by the hidden Markov model plus protein-based gene prediction FGENESH ? (Softberry, Inc.). Calculations ...


Tropical Plant Biology
Volume 4, Issue 3-4 , pp 217-227 DOI: 10.1007/s12042-011-9083-4

Molecular and Cytological Characterization of Centromeric Retrotransposons in a Wild Relative of Rice, Oryza granulata

Dongying Gao, Zhiyun Gong, Rod A. Wing, Jiming Jiang, Scott A. Jackson
1. Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, 111 Riverbend Rd., Athens, GA, 30602, USA 2. Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA

... In order to generate the phylogenetic tree with the conserved RT domains of LTR retrotransposons, the internal sequences from OGRetro9 and other 30 retroelements were annotated with FGENESH (http://linux1.softberry.com/berry.phtml) and GENEMARK (http://exon.gatech ...


BMC Evolutionary Biology
2011, 11:263 doi:10.1186/1471-2148-11-263

Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis

Turchetto-Zolet et al.,
1 Programa de Pos-Graduacao em Genetica e Biologia Molecular, Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Brazil 2 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Brazil

... The structural organization of the DGAT genes was determined after alignment of genomic DNA and cDNA and EST sequences. Genomic sequences were also analyzed in the FGENESH gene structure prediction program http://www.softberry.com/ webcite[58]. ...


BMC Plant Biology
2011, 11:26 doi:10.1186/1471-2229-11-26

Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

Masaki Fujisawa, Toshitsugu Nakano and Yasuhiro Ito
National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan

... Gene structures were predicted using the sim4 [60] and the FGENESH 2.6 [61] programs with a parameter for the tomato genome (available at the Softberry site: http://linux1.softberry.com/berry.phtml ...


Journal of Genetics and Genomics
Volume 38, Issue 7, 20 July 2011, Pages 315–325 DOI: 10.1016/j.jgg.2011.06.003

Use of methylation filtration and C0t fractionation for analysis of genome composition and comparative genomics in bread wheat

Bandopadhyay et al.,
a Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut 250004, India b Department of Biotechnology, Birla Institute of Technology, Mesra 835215, Ranchi, India

... Gene prediction was achieved using FGenesH (http://softberry.com/berry.phtml). 2.9. Fluorescence in situ hybridization (FISH). Four RD clones containing SSRs were used as probes, which were labeled with digoxigenin-11-dUTP by nick translation. ...


Theoretical and Applied Genetics
Volume 123, Issue 6 , pp 973-983 DOI: 10.1007/s00122-011-1640-6

Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L.

Li et al.,
1. Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China 2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA

... Gene annotation was performed with the computer program FGENESH (http://sunl.softberry.com/) and function prediction was conducted with BLASTx at the NCBI (National Center for Biotechnology Information) website (http://blast.ncbi.nlm.nih.gov). Molecular marker analysis ...


Theoretical and Applied Genetics
Volume 122, Issue 4 , pp 795-803 DOI: 10.1007/s00122-010-1487-2

Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster

Kang et al.,
1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China 3. Key Laboratory of Horticultural Crops Genetic Improvement, Ministry of Agriculture, 100081, Beijing, China

... Gene prediction was performed with the computer program BGF (http://bgf.genomics.org.cn) and verified by FGENESH (http://sunl.softberry.com/) (Salamov and Solovyev 2000), GENESCAN (http://genes.mit.edu/GENSCAN.html) (Burge and Karlin 1997), TwinScan (http://mblab ...


BMC Genomics
2011, 12:609 doi:10.1186/1471-2164-12-609

Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome

Dong et al.,
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China

... Then the obtained sequences were extended 10 kb each in the 5'-terminus and 3'-terminus respectively. Finally, the obtained putative autonomous helitrons were annotated by Fgenesh (http://linux1.softberry.com/berry.phtml webcite). ...


Agricultural Sciences in China
Volume 10, Issue 4, April 2011, Pages 481–489 DOI: 10.1016/S1671-2927(11)60028-X

Characterization of Zm26Sub5 and Its Potential Roles in Regulating Pollen Fertility of S-CMS in Maize

Zheng-feng ZHANG a, b, Yong-lian ZHENG b
a College of Life Science, Huazhong Normal University, Wuhan 430079, P.R. China b National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P.R. China

... embl-heidelberg.de/Alignment/). Gene prediction for the Zm26Sub5 DNA sequence was carried out, analyzing introns, exons, and poly(A), with the FGENESH 2.6 program (http://www.softberry.com/all/ htm). The protein encoded ...


The Plant Journal
2011, 65: 230–243. doi: 10.1111/j.1365-313X.2010.04414.x

Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs.

Riely et al.,
1 Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA 2 Beijing Forestry University, Beijing, China

...Bacterial artificial chromosomes identified as containing possible RopGEFs were analyzed using softberry fgenesh gene prediction tools to identify possible open reading frames in MtRopGEFs (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ...


Molecular and Cellular Biochemistry
Volume 357, Issue 1-2 , pp 263-274 DOI: 10.1007/s11010-011-0897-z

Alternative promoter usage and differential expression of multiple transcripts of mouse Prkar1a gene

Abdul Rouf Banday, Shafquat Azim, Mohammad Tabish
1. Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, 202002, India

... mit.edu/GENSCAN.html), GeneSplicer (http://cbcb.umd. edu/software/GeneSplicer/), FGENESH (http://www.soft berry.com/berry.phtml). Alignment analysis was carried out using the Gene stream Align tool (http://www2.igh.cnrs. ...


Theoretical and Applied Genetics
Volume 122, Issue 7 , pp 1247-1264 DOI: 10.1007/s00122-011-1528-5

Molecular basis of seed lipoxygenase null traits in soybean line OX948

Reinprecht et al.,
1. Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada 3. Agriculture and Agri-Food Canada, Greenhouse and Processing Crops Research Centre, Harrow, ON, N0R 1G0, Canada

... 2007) during the current study. The gene structure was also analyzed with the FGenesh 2.6 available at http://www. linux1.softberry.com (Salamov and Solovyev 2000). Translation of nucleotide sequences was generated on ExPASy (http://www.expasy.ch/tools/dna.html). ...


Plant Biotechnology Reports
Volume 5, Issue 4 , pp 331-344 DOI: 10.1007/s11816-011-0187-y

Isolation of an Rx homolog from C. annuum and the evolution of Rx genes in the Solanaceae family

Shi et al.,
1. Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea 2. Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

... GENESCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://linux1.softberry.com/ berry.phtml) were used for BAC sequence annotation of a Rx1-containing BAC from potato, a CapRGC-containing BAC from pepper, and a LaRGC-containing BAC from tomato. ...


New Phytologist
2011, 192: 713–726. doi: 10.1111/j.1469-8137.2011.03824.x

Conservation and clade-specific diversification of pathogen-inducible tryptophan and indole glucosinolate metabolism in Arabidopsis thaliana relatives.

Bednarek et al.,
1 Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Carl-von-Linne-Weg 10, D-50829 Koln, Germany 2 Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland

... To predict the open reading frames (ORFs) from the genomic candidate regions, Fgenesh (http://www.softberry.com) was used with parameters optimized for A. thaliana. The predicted proteins were aligned using ClustalW and visualized using Jalview (Waterhouse et al., 2009). ...


PLoS Genet
7(4): e1002029. doi:10.1371/journal.pgen.1002029

The Phylogenetic Origin of oskar Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola.

Lynch et al.,
Affiliation: Institute for Developmental Biology, University of Cologne, Cologne, Germany Department of Biology, McGill University, Montreal, Canada

...The genomic region surrounding the region showing homology to Osk was used as input into FgenesH using the Apis model at http://linux1.softberry.com/ to predict an Osk sequence, ...


Mobile DNA
2011, 2:12 http://www.mobilednajournal.com/content/2/1/12

Crypton transposons: identification of new diverse families and ancient domestication events

Kenji K Kojima and Jerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA

...We predicted exon-intron boundaries with the aid of SoftBerry FGENESH: http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind...


Genetica
Volume 139, Issue 4 , pp 489-496 DOI: 10.1007/s10709-011-9569-x

Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp

Dupuy et al.,
1. Institut de Recherche sur la Biologie de l’Insecte, UMR CNRS 6035, Universite F. Rabelais, UFR Sciences et Techniques, Parc Grandmont, 37200, Tours, France

... The hit was considered significant when the e-value was lower than 10-4. Open reading frames (ORFs) were identified using FGENESH (http://linux1.softberry.com) and putative ORFs were confirmed and adjusted if necessary through alignments with T. castaneum Maverick ...


Nature
478, 119–122 (06 October 2011) doi:10.1038/nature10431

Control of flowering and storage organ formation in potato by FLOWERING LOCUS T

Navarro et al.,
Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC. Calle Darwin 3, 28049 Madrid, Spain Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan

... The best genome matches (Supplementary Table 2)were downloaded and open reading frames were predicted using FGENESH (http://linux1.softberry.com/berry.phtml) and ORF Finder ...


BMC Evolutionary Biology
2011, 11:219 doi:10.1186/1471-2148-11-219

A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2

Fan et al.,
1 Laboratory of Yeast Genetics and Molecular Biology, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China 2 Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China

...The splicing pattern was verified using the FGENESH and FGENESH_GC programs provided at the Softberry website...


PLoS ONE
(2011) 6(8): e22046. doi:10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs.

Zhang et al.,
Department of Biology, University of Padua, Padova, Italy, Abteilung fur Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universitat zu Kiel, Kiel, Germany

...To ensure correct gene structures of all putative GPCR genes, we predicted gene structures using GENSCAN [97], [98] and predictions were repeated using GENOMESCAN [97], [98], GENEWISE [99] and FGENESH/FGENESH+ [31]. Intron-exon structures were determined with the aid of GENEWISE [99] and/or PROT_MAP module of the Softberry software suite (website: www.softberry.org). ...


MPMI
Vol. 24, No. 1, 2011, pp. 79–90. doi:10.1094/ MPMI -06-10-0131

TaDAD2, a Negative Regulator of Programmed Cell Death, Is Important for the Interaction Between Wheat and the Stripe Rust Fungus

Wang et al.,
1 College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China; 2 College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China;

...The HsDAD (Homo sapiens) was employed as the outgroup control for the construction of phylogenetic trees. Gene structure was predicted by FGENESH....


PLoS Genet
(2011), 7(8): e1002230. doi:10.1371/journal.pgen.1002230

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea.

Amselem et al.,
Unite de Recherche Genomique – Info, UR1164, INRA, Versailles, France, Biologie et Gestion des Risques en Agriculture – Champignons Pathogenes des Plantes, UR1290, INRA, Grignon, France Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

...For S. sclerotiorum and B. cinerea B05.10, gene structures were predicted using a combination of FGENESH and GENEID....


Molecular Ecology
(2011), 20: 2603–2618. doi: 10.1111/j.1365-294X.2011.05119.x

Characterization of a genomic divergence island between black-and-yellow and gopher Sebastes rockfishes.

BUONACCORSI et al.,
1 Juniata College, 1700 Moore St. Huntingdon, PA 16652, USA 2 Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Road, Hagerman, ID 83332, USA

... The sequenced region was manually annotated using ab initio gene predictions from Genscan (Burge & Karlin 1997) and FgenesH (SoftBerry; Fish gene model). Microsatellites were identified using Tandem Repeat Finder (Benson 1999). ...


Nature Biotechnology
29, 922–927 (2011) doi:10.1038/nbt.1976

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.

Berka et al.,
Novozymes, Inc., Davis, California, USA. US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.

... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly; cDNA-based EST_map (http://www.softberry.com/) seeded ...


Plant Physiology
October 2011 vol. 157 no. 2 937-946 DOI: 10.1104/pp.111.174912

Evolution of the S-Locus Region in Arabidopsis Relatives

Ya-Long Guo 2*, Xuan Zhao 2, Christa Lanz and Detlef Weigel
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany

... Annotation of the BAC sequences was performed using FGENESH (http://linux1. softberry.com/berry.phtml). The annotation was confirmed by ...


Nature Communications
2, Article number: 202 doi:10.1038/ncomms1189

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Rouxel et al.,
INRA-Bioger, UR1290, Avenue Lucien Bretignieres, BP 01, Thiverval-Grignon F-78850, France. Murdoch University, South Street, Murdoch, Western Australia 6150, Australia.

...The EuGene prediction pipeline v. 3.5a (ref. 48), which integrates ab initio (Eugene_IMM, SpliceMachine and Fgenesh 2.6 (www.softberry.com)) and similarity methods (BLASTn, GenomeThreader, BLASTx), was used to predict gene models. ...


Nature Genetics
43, 228–235 (2011) doi:10.1038/ng.769

The draft genome of the parasitic nematode Trichinella spiralis

Mitreva et al.,
The Genome Center, Washington University School of Medicine, St. Louis, Missouri, USA. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.

...Protein-coding genes were predicted using a combination of ab initio programs47 and FgenesH (Softberry, Corp) and the evidence-based program EAnnot48. ...


Theoretical and Applied Genetics
Volume 122, Issue 3 , pp 459-470 DOI: 10.1007/s00122-010-1460-0

Characterization and genetic analysis of a low-temperature-sensitive mutant, sy-2, in Capsicum chinense

An et al.,
1. Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul, 151-921, Korea 2. Key Laboratory of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Beijing Key Lab of Crop Genetic Improvement, China Agriculture University, Beijing, 100094, China

... C2_At1g09070. In the sequence, 51 genes were predicted by gene prediction FGENESH (http://linux1.softberry. com) and blastx (http://blast.ncbi.nlm.nih.gov). There were several candidate genes including five lipoxygenase genes, ...


The Plant Journal
(2011), 65: 745–756. doi: 10.1111/j.1365-313X.2010.04461.x

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

Quraishi et al.,
1 INRA/Universite Blaise Pascal UMR 1095 GDEC, Domaine de Crouelle, 234 Avenue du Brezet, 63100 Clermont-Ferrand, France 2 BIOGEMMA, 8 Rue des Freres Lumiere, 63028 Clermont-Ferrand Cedex 2, France

... nih.gov/) and SwissProt databases (http://expasy.org/sprot/), with the results of two gene predictor programs, Eugene (Matheet al., 2002) with the rice (Oryza sativa) training version and FgeneSH (Salamov and Solovyev, 2000) with default parameters (http://sun1.softberry.com/). ...


Plant Physiology October
2011 vol. 157 no. 2 757-769 DOI: 10.1104/pp.111.181990

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

Guo et al.,
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany

... Gordon et al., 1998). Primer walking and PCR were used to fill or polish gaps and ambiguous regions. Annotation was performed using FGENESH and FGENESH+ (http://linux1.softberry.com/berry.phtml). Spidey (http://www.ncbi ...


BMC Genomics
2011, 12:142 doi:10.1186/1471-2164-12-142

Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

Tian et al.,
1 Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA 2 Arizona Genomics Institute, The University of Arizona, Tucson, AZ 85721, USA

... Putative gene models were predicted using the FGENESH program with the monocot training set (http://www.softberry.com webcite), and were further investigated to determine whether they are actually genes following described previously criteria [6]. Truncated gene fragments ...


The Plant Journal
(2011), 68: 777–787. doi: 10.1111/j.1365-313X.2011.04728.x

Rice 14-3-3 protein (GF14e) negatively affects cell death and disease resistance.

Manosalva, P. M., Bruce, M. and Leach, J. E.
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.

... Throughput Genomic Sequences (HTGS) database. The fgenesh program (http://www.softberry.com/berry.phtml) was used to predict 14-3-3 gene members from significant rice BAC hits. All sequences corresponding to various ...


Genomics
Volume 97, Issue 5, May 2011, Pages 313–320 DOI: 10.1016/j.ygeno.2011.02.007

Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage

Lin et al.,
a Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA b Center for Genomics and Biocomputing, College of Sciences, Hebei Polytechnic University, Tangshan, Hebei, 063000, China

...Genes were identified from BAC sequences using FGENESH (http://linux1.softberry.com/berry.phtml). ...


BMC Evolutionary Biology
2011, 11:78 doi:10.1186/1471-2148-11-78

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture

Cigliano et al.,
1 CNR - National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Universita 133, 80055 Portici. Italy 2 DISSPAPA, Dept. of Soil, Plant and Environmental Sciences, University of Naples "Federico II", Via Universita 100, 80055 Portici. Italy

... Germany). PSL1 gene structure and cDNA predictions were carried out using FGENESH online tool (http:/ / linux1.softberry.com/ berry.phtml?topic=fgenesh&group=pro grams&subgroup=gfind webcite) selecting Tomato as organism. ...


BMC Research Notes
2011, 4:518 doi:10.1186/1756-0500-4-518

Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida)

Maik Klie and Thomas Debener
Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universitat Hannover, Herrenhauser Str. 2, 30419 Hannover, Germany

...Open reading frames and 5'and 3' UTR regions were predicted using the FGENESH algorithm [34] with specifications for dicot plants....


Aging Cell
(2011), 10: 896–907. doi: 10.1111/j.1474-9726.2011.00727.x

Alternative splicing factor or splicing factor-2 plays a key role in intron retention of the endoglin gene during endothelial senescence.

Blanco, F. J. and Bernabeu, C.
Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), and Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), c/Ramiro de Maeztu 9, 28040 Madrid, Spain

... Genome Bioinformatics (http://genome.ucsc.edu/). Then, the FSPLICE and FGENESH tools were used to predict exons and introns in the DNA sequences (http://linux1. softberry.com/berry.phtml). The Transeq tool at the European ...


PLoS Pathog
(2011), 7(7): e1002137. doi:10.1371/journal.ppat.1002137

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens.

Klosterman et al.,
USDA-ARS, Salinas, California, United States of America University of California, Davis, California, United States of America

...Protein-encoding genes were annotated using a combination of manually curated genes, in addition to EST BLAST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com), and ...


PLoS Negl Trop Dis
(2011), 5(10): e1340. doi:10.1371/journal.pntd.0001340

Characterisation of the Trichinella spiralis Deubiquitinating Enzyme, TsUCH37, an Evolutionarily Conserved Proteasome Interaction Partner.

White et al.,
Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London, United Kingdom Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America

...Contig 1.2 was analysed by 4 different gene prediction programmes: AUGUSTUS [24], GenemarkHMM [31], SNAP [32] and Fgenesh [33]. ...


The Plant Cell May
2011 vol. 23 no. 5 1861-1875 DOI: 10.?1105/?tpc.?111.?085456

A Small Zinc Finger Thylakoid Protein Plays a Role in Maintenance of Photosystem II in Arabidopsis thaliana

Yan Lu a, 1, David A. Hall a and Robert L. Last a,b,2
aDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 bDepartment of Plant Biology, Michigan State University, East Lansing, Michigan 48824

...Complete genomic sequence (including 500 bp upstream and downstream of the original partial sequence) was used to predict new gene structures with the FGENESH program (a Hidden Markov Model-based gene prediction program; http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind)....


PLoS ONE
(2011), 6(3): e17505. doi:10.1371/journal.pone.0017505

Elucidation of Functional Markers from Aspergillus nidulans Developmental Regulator FlbB and Their Phylogenetic Distribution.

Cortese MS, Etxebeste O, Garzia A, Espeso EA, Ugalde U
Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastian, Spain, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain Department of Cellular and Molecular Medicine, Centro de Investigaciones Biologicas (CSIC), Madrid, Spain

...and Fgenesh (Softberry) [71] were considered along with manual verification of splice sites....


Genome Biology
2011, 12:R48 doi:10.1186/gb-2011-12-5-r48

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Zuccolo et al.,
1 Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA 2 Department of Plant Biology, University of Georgia, 4504 Miller Plant Sciences, Athens, GA 30602, USA

...FGENESH [63] annotations for the Amborella contigs were included on the horizontal axes of the dot plots. ...


Plant Physiology
October 2011 vol. 157 no. 2 770-789 DOI: 10.?1104/?pp.?111.?179648

The Tomato Terpene Synthase Gene Family

Falara et al.,
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109–1048 (V.F., T.A.A., T.T.H.N., I.S., Y.M., M.E.B., E.P.); Department of Plant Physiology, Swammerdam Institute of Life Sciences, 1098 XH Amsterdam, The Netherlands (E.A.S., P.M.B., R.C.S.)

...he FGENESH gene prediction tool (www.softberry.com) was used for initial annotation of the predicted tomato TPS genes....


PLoS Pathog
(2011), 7(11): e1002348. doi:10.1371/journal.ppat.1002348

Multiple Candidate Effectors from the Oomycete Pathogen Hyaloperonospora arabidopsidis Suppress Host Plant Immunity. PLoS Pathog 7(11): e1002348. doi:10.1371/journal.ppat.1002348

Fabro et al.,
The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom School of Life Sciences, Warwick University, Wellesbourne, United Kingdom

...ORFs from ATG to Stop codon were identified using FgenesH (www.softberry.com) and ...


BMC Plant Biology
2011, 11:20 doi:10.1186/1471-2229-11-20

ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs

Ricachenevsky et al.,
1 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, P.O.Box 15005, Porto Alegre, 91501-970, Brazil 2 Departamento de Botanica, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, Porto Alegre, 91501-970, Brazil

...Two unnanotated ZIFL genes from Zea mays were predicted using Fgenesh (http://www.softberry.com ...


FGENESH 2010

Cytogenet Genome Res
2011;132:55-63 (DOI: 10.1159/000319491)

Sequence of a Turkey BAC Clone Identifies MHC Class III Orthologs and Supports Ancient Origins of Immunological Gene Clusters

L.D. Chaves a, b, S.B. Krueth a, M.M. Bauer a, K.M. Reed a
aDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minn., and bNational Jewish Health, Division of Allergy and Clinical Immunology, Department of Medicine, Denver, Colo., USA

... Sequences were analyzed with the basic local alignment search tool (BLAST), GENESCAN (http://genes.mit.edu/GENSCAN.html) and Softberry FGENESH (http://linux1.softberry.com/ all.htm) to identify putative transcripts and homologies to known genes. ... 


Gene
Volume 452, Issue 2, 1 March 2010, Pages 45-53, doi:10.1016/j.gene.2009.11.001

Comparative genomics identifies new alpha class genes within the avian glutathione S-transferase gene cluster

Ji Eun Kim a, Miranda M. Bauer b, Kristelle M. Mendoza b, Kent M. Reed b and Roger A. Coulombe Jr. a,
a Department of Veterinary Sciences and Graduate Toxicology Program, Utah State University, Logan, UT 84322, USA b Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA

.. 2.4. Gene identification and annotation. The assembled sequence was analyzed with Softberry FGENESH (http://linux1.softberry.com/all.htm) and the basic local alignment search tool (BLAST) to identify putative transcripts and homologies to known genes. ... 


Gene
Volume 468, Issues 1-2, 15 November 2010, Pages 41-47 doi:10.1016/j.gene.2010.08.003

Two conserved Z9-octadecanoic acid desaturases in the red flour beetle, Tribolium castaneum

Irene Horne a, Nerida Gibb a, Katherine Damcevski a, Karen Glovera and Victoria S. Haritos a
a CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia

... were obtained. Each of the contigs was then subjected to a gene prediction program in Softberry (http://www.softberry.com/cgi- bin/programs/gfin/fgenesh) using parameters for Brugia malaya and Caenorhabditis elegans. 2.2 ... 


Journal of Invertebrate Pathology
Volume 105, Issue 2, October 2010, Pages 156-163 doi:10.1016/j.jip.2010.06.003

Transient transcription of a putative RNase containing BEN domain encoded in Cotesia plutellae bracovirus induces an immunosuppression of the diamondback moth, Plutella xylostella

Bokri Park and Yonggyun Kim
Department of Bioresource Sciences, Andong National University, Andong 760-749, Republic of Korea

... 17 18 2.2. Gene prediction using bioinformatic tools 19 20 Open reading frame (ORF) was predicted from a viral genome segment using 21 FGENESH program (Softberry, Inc., Mount Kisco, NY, USA) by access to 22 http://linux1.softberry.com/berry.phtml?topic=index&group ... 


Genome
Volume 53, Number 1, 1 January 2010 , pp. 55-67(13)

Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis

Parida, Swarup K.; Yadava, Devendra K.; Mohapatra, Trilochan

... Also, unigenes were checked using software tools such as FGENESH (Softberry, Inc., Mount Kisco, New York; www. softberry.com), ORF Finder (Stothard 2000; http:// bioinformatics.org/sms/orf_find.html), and UTRScan (http ... 


Bioinformatics
2010, 26 (12): 1488-1492. doi: 10.1093/bioinformatics/btq167

Ergatis: a web interface and scalable software system for bioinformatics workflows

Orvis et al.,
1 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 2 J. Craig Venter Institute, Rockville, MD, USA

... Ergatis contains components for over a dozen different gene prediction programs, such as GeneWise (Birney et al., 2004), GeneMark (Besemer and Borodovsky, 2005) and FGENESH (SoftBerry), as well as RNA prediction. ... SoftBerry. "Gene finding in Eukaryota.". ... 


Mol Biol Evol
2010, 27 (11): 2487-2506. doi: 10.1093/molbev/msq133

Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum

Sanyal et al.,
1Department of Agronomy, Purdue University 2Department of Plant Sciences, BIO5 Institute, Arizona Genomics Institute, University of Arizona, Tucson

... The sequences were then annotated for genes using a combination of ab initio prediction programs FGENESH (www.softberry.com, Salamov and Solovyev 2000) and Page 8. 8 ... (www.softberry.com, Salamov and Solovyev 2000) and with previous annotation. We ... 


Nucl. Acids Res
2010 doi: 10.1093/nar/gkq1016

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

Wong et al.,
1Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D-85764 Neuherberg, 2Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg,

... Based on this set, all gene loci in FGDB v3.1 were re-annotated using a pipeline including (i) Fgenesh with different matrices (www.softberry.com); (ii) GeneMark-ES (8); (iii) Augustus with ESTs, precedingly annotated Fusarium models and/or Neurospora crassa protein ...


PLoS ONE
5(3): e9620. doi:10.1371/journal.pone.0009620

Morphological and Genomic Characterization of Filobasidiella depauperata: A Homothallic Sibling Species of the Pathogenic Cryptococcus Species Complex

Marianela Rodriguez-Carres, Keisha Findley, Sheng Sun, Fred S. Dietrich, Joseph Heitman
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America

... Assembled sequences were subsequently annotated employing the gene predictor software FGENESH from SoftBerry© and using as reference current gene predictions in C. neoformans (http://linux1.softberry.com/berry.phtml??topic=fgenesh&group=programs&subgroup=gf ... 


Mol Biol Rep.
2010 Feb;37(2):801-8. Epub 2009 Jul 4

Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from Upland cotton (Gossypium hirsutum L.)

Yang L, Zhu H, Guo W, Zhang T
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.

... The remaining non- redundant sequences were assembled by CAP3 assembly tool [24] with default parameter. Potential genes of BAC sequences originated from the G. hirsutum database were predicted by a program: FGENESH (http://www.softberry. ... 


J Mol Evol.
2010 Jan 1. [Epub ahead of print]

Strong Positive Selection Drives Rapid Diversification of R-Genes in Arabidopsis Relatives

Chen Q, Han Z, Jiang H, Tian D, Yang S.
State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.

... the gene-finding programs FGENESH (http://www. softberry.com/) and GENSCAN (http://genes.mit.edu/ genescan.html/) to obtain information on complete open reading frames. To exclude potentially redundant candidate NBS ... 


Eukaryotic Cell
January 2010, p. 164-172, Vol. 9, No. 1 doi:10.1128/EC.00194-09

Evolutionary Dynamics of Mating-Type Loci of Mycosphaerella spp. Occurring on Banana

Mahdi Arzanlou, 1,2,3 Pedro W. Crous, 1,2 and Lute-Harm Zwiers 1
Evolutionary Phytopathology, CBS-KNAW Fungal Biodiversity Center, Utrecht 3508 AD, The Netherlands,1 Wageningen University and Research Center (WUR), Laboratory of Phytopathology, Wageningen 6708 PB, The Netherlands,2

... reading frames (ORFs) and intron positions were predicted by comparing the sequence data with known MAT sequences from other filamentous fungi, as well as by means of the FGENESH gene prediction module from the MOLQUEST software package (Softberry, Inc., Mount ... 


Plant Molecular Biology Reporter
Volume 28, Number 1, March 2010 , pp. 152-161(10) DOI: 10.1007/s11105-009-0134-z

Identification of NBS-Type Resistance Gene Homologs in Tobacco Genome

Xiaodong et al.,
1: Institute of Crop Science, Zhejiang University, Hangzhou, 310029, China 2: Joint Laboratory of Tobacco Bioinformatics, Yunnan Institute of Tobacco Science, Yuxi, 653100, China,

... 2006) for sequence cleaning and assembly. FGENESH was used to perform gene prediction (http://www.softberry.com) (Salamov and Solovyev 2000). HMMER (Eddy 1998) was used to search protein sequences Plant Mol Biol Rep (2010) 28:152–161 153 Page 3. ... 


J. Agric. Food Chem.
2010, 58 (5), pp 3184–3190 DOI: 10.1021/jf904367r

An Acidophilic and Acid-Stable b-Mannanase from Phialophora sp. P13 with High Mannan Hydrolysis Activity under Simulated Gastric Conditions

Zhao et al.,
Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China

... sequence. Sequence Analysis The exon-intron structure of the full-length mannanase gene was predicted using GENESCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com/berry.phtml/). The ... 


New Phytologist
Special Issue: Plant polyploidy

Volume 186, Issue 1, pages 228–238, April 2010 DOI: 10.1111/j.1469-8137.2009.03164.x

Tandem duplication of the FLC locus and the origin of a new gene in Arabidopsis related species and their functional implications in allopolyploids

Nah, G. and Jeffrey Chen, Z.
1. Section of Molecular Cell and Developmental Biology 2. Institute for Cellular and Molecular Biology 3. Section of Integrative Biology 4. Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA

... Sonnhammer & Durbin, 1995). The genomic sequences were annotated using fgenesh (http://www.softberry.com), a gene prediction software program for A. thaliana genome annotation (Swarbreck et al., 2008). The predicted genes ... 


Funct Integr Genomics.
2010 May;10(2):241-51. Epub 2009 Dec 12

Recruitment of closely linked genes for divergent functions: the seed storage protein (Glu-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.)

Wang ZN, Huang XQ, Cloutier S.
Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, Canada, R3T 2M9.

... ricegaas.dna.affrc. go.jp/) using the gene prediction algorithm of FGENESH Funct Integr Genomics Page 3. (http://www.softberry.com/) and GENESCAN (http://gene mark.mit.edu/GENESCAN.htm). The predicted gene sequences ... 


Journal of Basic Microbiology
Volume 50, Issue 1, pages 59–71, February 2010 DOI: 10.1002/jobm.200900113

Adenylyl cyclase regulates heavy metal sensitivity, bikaverin production and plant tissue colonization in Fusarium proliferatum

Gabor Kohut 1, Brigitta Olah 1, Attila L. Adam 1, Jorge Garcia-Martinez 2, Laszlo Hornok Prof. 1
1. Agricultural Biotechnology Center, Mycology Group of the Hungarian Academy of Sciences, Institute of Plant Protection, Szent Istvan University, Godollo, Hungary 2. Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain

... Biotechnology Centre (Godollo, Hungary). Se- quence data were analyzed with the Lasergene software package (DNAStar Inc., Madison, Wisconsin, USA) and the FGENESH program (http://www.softberry.com). Blast searches were ... 


Theor Appl Genet.
2010 Apr;120(6):1099-106. Epub 2009 Dec 24

Fine mapping of pepper trichome locus 1 controlling trichome formation in Capsicum annuum L. CM334.

Kim et al.,
Department of Plant Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, South Korea.

... 2003). Repeat sequences were filtered by RepeatMasker (http://www. repeatmasker.org) and JDotter (http://athena.bioc.uvic.ca). The gene coding regions were predicted by FGENESH (http://linux1.softberry.com) or GENESCAN (http://genes. ... 


Eukaryotic Cell
January 2010, p. 46-58, Vol. 9, No. 1 doi:10.1128/EC.00259-09

Organization and Evolutionary Trajectory of the Mating Type (MAT) Locus in Dermatophyte and Dimorphic Fungal Pathogens

Wenjun Li, 1 Banu Metin, 1 Theodore C. White ,2 and Joseph Heitman 1
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina,1 Seattle Biomedical Research Institute, Seattle, Washington2

... Putative genes in the MAT locus and flanking regions were predicted by using a combination of primary annotation from the Broad Institute, GeneMark (37), BLAST (1), ORF Finder (http://www.ncbi.nlm.nih.gov/projects/gorf/), and FGENESH (http://linux1.softberry.com/berry.phtml ... 


Molecular Plant Pathology
2010, 11: 395–407. doi: 10.1111/j.1364-3703.2010.00612.x

The two-component histidine kinase Fhk1 controls stress adaptation and virulence of Fusarium oxysporum

RISPAIL, N. and DI PIETRO, A
Departamento de Genetica, Universidad de Cordoba, Campus de Rabanales Edificio Gregor Mendel C5, 14071 Cordoba, Spain

... ing the complete fhk1 gene, including the promoter, coding region and terminator, was sequenced manually, revealing an open reading frame of 3882 bp interrupted by five putative introns, according to the Fgenesh 2.6 prediction server (http:// linux1.softberry.com/berry.phtml ... 


Funct Integr Genomics
2010 Mar;10(1):111-22. Epub 2009 Aug 2

Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins

Gu YQ, Wanjugi H, Coleman-Derr D, Kong X, Anderson OD.
Western Regional Research Center, United States Department of Agricultural-Agricultural Research Service, Albany, CA 94710, USA. yong.gu@ars.usda.gov

... 2003) and wheat A genome (BAC AY494981 and DQ537335, Gu et al. 2004, 2006, respectively). FGENESH (http://www.softberry.com/nucleo.html) and GEN- ESCAN (http://genemark.mit.edu/GENESCAN.htm) were used for gene prediction. ... 


Molecular Breeding
Volume 26, Number 2, August 2010 , pp. 275-292(18)

Genic markers for wild abortive (WA) cytoplasm based male sterility and its fertility restoration in rice

Ngangkham, Umakanta et al.,
1: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India 2: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

... msu.edu/pseudomolecules) and indica cultivar 93–11 (Beijing Rice Information System, http://rice.genomics. org.cn/rice) were downloaded and annotated using FGENESH (http://sun1.softberry.com/berry.phtml) gene prediction software to identify protein encoding genes. ... 


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184-194 doi:10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

ATiago M. Martins a, b, Virgilio E. do Rosario b and Ana Domingos a, b
Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E 1e-04 was adopted for 93 the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with 94 multiple exons was predicted using the FGENESH and FGENESH+ software 95 (http://www.softberry.com). ... 


Mol Genet Genomics.
2010 May;283(5):427-38. Epub 2010 Mar 9

Unique evolutionary pattern of numbers of gramineous NBS-LRR genes

Li et al.,
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.

... with Xanking regions of 5,000–10,000 bp on both sides, were annotated using the gene-finding programs FGENESH with the monocot training set (http://www.soft- berry.com/) and GENSCAN with the maize training set (http://genes.mit.edu/GENSCAN.html) to obtain informa ...


Mol Biol Evol
2010 doi: 10.1093/molbev/msq156

Tracing the evolution of the floral homeotic B- and C-function genes through genome synteny

Barry Causier *,1, Rosa Castillo 2,4, Yongbiao Xue 3, Zsuzsanna Schwarz-Sommer 2 and Brendan Davies 1
1 Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom 2 Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne-Weg 10, 50829 Koln, Germany

... Lukashin and Borodovsky 1998) (each using the Arabidopsis dataset, with default settings), and FGENESH (www.softberry.com) (using both Arabidopsis and tobacco datasets, with default settings). In most cases each algorithm predicted a similar ... 


Veterinary Immunology and Immunopathology
Volume 137, Issues 1-2, 15 September 2010, Pages 176-180 doi:10.1016/j.vetimm.2010.04.018

Polymorphism of sheep MHC Class IIb gene TAPASIN

N. Siva Subramaniam a, E.F. Morgan a, C.Y. Lee a, J.D. Wetherall a and D.M. Groth a
Western Australian Biomedical Research Institute (WABRI) & Centre for Health Innovation Research Institute, School of Biomedical Sciences, Curtin University of Technology, Perth, Western Australia 6845, Australia

... A consensus genetic structure for sheep 108 TAPASIN was determined from analysis of the predictions from GENSCAN (Burge & 109 Karlin 1997) Burge and Karlin, 1997), TWINSCAN (Korf et al. 2001) and 110 FGENESH (http://www.softberry.com). ... 


Theor Appl Genet.
2010 Feb;120(4):709-20. Epub 2009 Nov 3.

Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species

Fu et al.,
National Maize Improvement Center of China, Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, Yuanmingyuan West Road, Haidian, Beijing, China.

... Gene structure was predicted separately for each species using the soft- ware packages FGENESH (http://linuxl.softberry.com) and NNPP (http://www.fruitfly.org). Alignments were per- formed among all species with the ClustalX version 8.1 (Thompson et al. ... 


The Journal of Immunology
May 1, 2010 vol. 184 no. 9 5038-5046 doi: 10.4049/?jimmunol.0903374

Intron-Containing Type I and Type III IFN Coexist in Amphibians: Refuting the Concept That a Retroposition Event Gave Rise to Type I IFNs

1. Zhitao Qi*†, Pin Nie*, Chris J. Secombes‡ and Jun Zou‡
*State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei; †Chemical and Biological Engineering College, Yancheng Institute of Technology, Jiangsu, China

... ca.expasy.org/tools). Putative transcripts were predicted from the genome sequences using the GenScan program (http://genes/mit.edu/GENSCAN.html) and the Fgenesh program (www.softberry.com). Signal peptides were ... 


Molecular Breeding
Volume 26, Number 2, August 2010 , pp. 325-338(14)

SNP haplotypes of the BADH1 gene and their association with aroma in rice (Oryza sativa L.)

Singh, Anuradha et al.,
1: Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India 2: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

... work well. The position of exons and introns were identified using gene prediction software FGENESH (www.softberry.com) and verified manually by checking against the full length cDNA sequence of the BADH1 gene. The ... 


Theor Appl Genet.
2010 May;120(7):1443-50. Epub 2010 Jan 2010

Fine mapping of a resistance gene to bacterial leaf pustule in soybean

Kim DH, Kim KH, Van K, Kim MY, Lee SH
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea

... Composite interval mapping (CIM) was performed by Qgene V. 4.2.2 (Joehanes and Nelson 2008) with scan interval 1. Gene annotation was conducted with gene prediction program FGENESH (http:// www.softberry.ru) against Arabidopsis database. ... 


Plant Science
Volume 179, Issue 4, October 2010, Pages 399-406 doi:10.1016/j.plantsci.2010.06.017

Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species

Tang et al.,
a State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093 Nanjing, China b Department of Life Science, Lianyungang Teacher's College, 222006 Lianyungang, China

... Then the nucleotide sequences of candidate Ser/Thr/Tyr kinase genes, together with flanking regions of 5,000-10,000 bp at both sides, were annotated using the gene-finding programs FGENESH (http://www.softberry.com/) and GENSCAN (http://genes.mit.edu/genescan.html ... 


Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
Volume 5, Issue 2, June 2010, Pages 151-156 doi:10.1016/j.cbd.2010.03.006

Novel isoform of the Xenopus tropicalis PKA catalytic alpha subunit: An example of alternative splicing

Mohammad Tabish, Vladimir I. Rodionov
Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut 06032, USA

... Gene/Exon finding tools were used at HMMgene (http://www.cbs.dtu.dk/services/HMMgene), Genescan (http://genes.mit.edu/ GENSCAN.html), GeneSplicer (http://cbcb.umd.edu/ software/GeneSplicer/), FGENESH (http://www.softberry.com/berry.phtml). ... 


Molecular breeding
2010, vol. 25, no2, pp. 187-201

Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper

Deuk et al.,
(1) Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea (2) Breeding and Research Station, Monsanto Korea, 363-955, Chungwon, Korea

... search using petunia Rf gene sequence as query. FGENESH program (www.softberry.com) was used to predict gene sequences from sequences of selected BAC clones. Among predicted fifteen genes, sequence of the first ... 


Plant Science
Volume 179, Issue 3, September 2010, Pages 257-266 doi:10.1016/j.plantsci.2010.05.012

Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily

Ming-Bing Zhou a, Jiang-Jie Lu a, Hao Zhonga, Xiang-Min Liu a and Ding-Qin Tang a
a The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, LinAn 311300, Zhejiang Province, PR China

.. The putative coding exons of these sequences, as well as those derived from our 114 PCR experiments, were predicted using web software of Netgene2 115 (http://www.cbs.dtu.dk/services/ NetGene2/) and FGENESH 116 (http://sun1.softberry.com/berry.phtml?topic ... 


Genome
Volume 53, Number 9, 1 September 2010 , pp. 658-666(9)

Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus

Dae-Won Kim et al.,

.. submit.html) (Benson 1999). We also searched for potential genes on the contig sequences using FGENESH (SoftBerry, Inc., Mount Kisco, New York), geneid (http://genome.imim. es/geneid.html), and GeneMark (http://exon.biology.gatech. edu/eukhmm.cgi). ...


Fungal Genetics and Biology
Volume 47, Issue 8, August 2010, Pages 663-671 doi:10.1016/j.fgb.2010.04.008

Phytophthora nicotianae transformants lacking dynein light chain 1 produce non-flagellate zoospores

Reena D. Narayan a, Leila M. Blackman a, Weixing Shan 1, a and Adrienne R. Hardham a
a Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia

... DNA sequences were 22 searched for introns using FGENESH 23 (http://linux1.softberry.com/ berry.phtml?topic=fgenesh&group=programs&subgroup24 =gfind). For phylogenetic analysis, homologues of DLC1 were retrieved from NCBI 25 and JGI databases. ... 


Plant Physiology Preview
Published on September 10, 2010; 10.1104/pp.110.163923

Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison to Thellungiella salsuginea (T. halophila) and Arabidopsis thaliana

Oh et al.,
1 University of Illinois Urbana-Champaign; 2 Purdue University

... An ab-initio ORF prediction with FGENESH(http://linux1.softberry.com/berry.phtml) identified 2,229 ORFs, ... The open reading frames (ORFs) in genomic sequences were predicted ab initio with FGENESH (http://www.softberry.com) adopting Arabidopsis parameters. ... 


BMC Plant Biol.
2010 Aug 19;10:183. doi:10.1186/1471-2229-10-183

Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds

Seabra AR, Vieira CP, Cullimore JV, Carvalho HG.
Instituto de Biologia Molecular e Celular da Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

... resources (http://www.medicago.org/genome/). Organization of both GS2 genes and prediction of MtGS2b coding sequence was carried out using the FGENESH2.6 software from Softberry (www.softberry.com). MtGS2a and MtGS2b amino acid sequences were ... 


PLoS ONE
2010 5(4): e9958. doi:10.1371/journal.pone.0009958

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA
1 United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America, 2 Cornell University, Department of Plant Breeding and Genetics, Ithaca, New York, United States of America

.. Genes of interest were placed on the physical-genetic map of maize using the BLAST tool implemented by the Maize Genome Sequencing Project [42]. Gene architecture predictions were made using the FGenesH tool as implemented by Softberry [46]. Statistical tests. ... 


Fish & Shellfish Immunology
Volume 29, Issue 4, October 2010, Pages 594-599 doi:10.1016/j.fsi.2010.06.004

Ig heavy chain genes and their locus in grass carp Ctenopharyngodon idella

Xiao et al.,
a State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China b Graduate School of the Chinese Academy of Sciences, Beijing 100039, China

... sequence. The software GENSCAN (http://genes.mit.edu/GENSCAN.html), 131 FGENESH (http://linux1.softberry.com/all.htm) and BLASTX 132 (http://blast.ncbi. nlm.nih.gov/Blast.cgi) were employed for the genome annotation. ... 


Molecular breeding
2010, vol. 25, no1, pp. 155-166

Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice

Channamallikarjuna et al.,
(1) National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012, New Delhi, India (2) Directorate of Rice Research, Andhra Pradesh, Hyderabad, India

... Nipponbare (www.ncbi.nlm.nih.gov) was used for gene prediction. FGENESH gene pre- diction software (www.softberry.com) was used to predict genes in this sequence. Predicted genes were functionally annotated by using BLASTp (bit- score C 100, E value B -20) software. ... 


Fungal Genetics and Biology
Volume 47, Issue 9, September 2010, Pages 761-772 doi:10.1016/j.fgb.2010.06.001

Characterization of the mating type (MAT) locus in the Phialocephala fortinii s.l. – Acephala applanata species complex

Pascal L. Zaffarano a, Angelo Duo a and Christoph R. Grunig a
a Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zurich, 8092 Zurich, Switzerland

... 184 185 2.5. Annotation of the MAT locus 186 187 Positions of open reading frames, transcription start and poly-A motifs in 188 sequences were predicted with FGENESH (http://linux1.softberry.com/ berry. 189 phtml?topic=fgenesh&group=programs&subgroup=gfind). ... 


Eukaryotic Cell
2010 doi:10.1128/EC.00161-10

Co-localization of Amanitin and a Candidate Toxin-Processing Prolyl Oligopeptidase in Amanita Basidiocarps

Hong Luo, Heather E. Hallen-Adams, John S. Scott-Craig, and Jonathan D. Walton
Department of Energy Plant Research Laboratory, Michigan State University, E. Lansing MI 48824

... AbPOPA and AbPOPB, and two hybridizing clones were sequenced completely. 11 FGENESH (www.softberry.com) was used to predict proteins ab initio using the 12 Coprinopsis cinerea model. Each predicted protein was then used to search GenBank nr 13 using BLASTP. ...


BMC Plant Biology
2010, 10:145doi:10.1186/1471-2229-10-145

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Hu et al.,
1 Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China 2 Current address: Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA

... putative pseudogenes or incorrect annotations, and manual reannotation was performed to correct and reannotate the putative NACs using online web server FGENESH (http://linux1.softberry.com/ berry.phtml) [59]. In this endeavor, seven sequences encoding only ... 


Bioorganic & Medicinal Chemistry
Volume 18, Issue 12, 15 June 2010, Pages 4542-4546 doi:10.1016/j.bmc.2010.04.058

Identification of csypyrone B1 as the novel product of Aspergillus oryzae type III polyketide synthase CsyB

Yasuyo Seshime a, †, Praveen Rao Juvvadi b, ‡, Katsuhiko Kitamoto b, Yutaka Ebizuka c and Isao Fujii a
a School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan b Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan

... These sequences were hand annotated by using FGENESH program (Softberry, Inc.) and/or GeneID program. 25 Acknowledgements We thank Dr. D. Wakana for measurement of the physicochemical properties of the compound, and Dr. T. Kushiro for helpful suggestions. ... 


PNAS
January 5, 2010 vol. 107 no. 1 472-477 doi: 10.1073/pnas.0908007107

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

Tang, Haibao,Bowers, John E.,Wang, Xiyin,Paterson, Andrew H.
aPlant Genome Mapping Laboratory and bDepartment of Plant Biology, University of Georgia, Athens, GA 30602

... set (Sbi1.4) from the Joint Genomics Institute (19), and the grapevine gene set from Genoscope (3). Two Musa balbisiana BACs (AC226052.1 and AC226053.1) were downloaded from GenBank, with putative gene models predicted using FGENESH (http://www.softberry.com). ... 


BMC Plant Biology
2010, 10:25 6doi:10.1186/1471-2229-10-256

Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

Qingpo Liu and Zhujun Zhu
College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou 311300, China

... Programs InterProScan [45] and Page 14. ConPred II [46] were utilized to detect conserved domains and predict the putative transmembrane regions (TMs), respectively. FgeneSH (http://linux1.softberry.com/) was employed to predict the gene structures of candidates identified. ...


BMC Plant Biology
2010, 10:180 doi:10.1186/1471-2229-10-180

Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia

Cegan et al.,
1 Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Kralovopolska 135, CZ-612 65 Brno, Czech Republic 2 Department of Plant Biology, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic

... software [48] (http://genes.mit.edu/GENSCAN.html) and FGENESH [49] (http://linux1.softberry. com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). ORFs were found with ORF Finder [50] (http://www.ncbi.nlm.nih.gov/projects/gorf/) and a ...


BMC Plant Biology
2010, 10:135 doi:10.1186/1471-2229-10-135

Transcriptional regulation of the grape cytochrome P450 monooxygenase gene CYP736B expression in response to Xylella fastidiosa infection

Cheng et al.,
1 San Joaquin Valley Agricultural Science Center, USDA-ARS 9611 South Riverbend Avenue, Parlier, CA 93648, USA 2 Department of Biology, California State University, Fresno, CA 93740, USA

... a grape genomic database (GenBank Accessions: AM475392.1, CAAP02000243. 1, CAAP02005006.1) using the BLAST (http://www.ncbi.nlm.nih.gov/) and FGENESH (http://www.softberry.com/berry.phtml) programs. A pair ...


BMC Genomics
2010, 11:179 doi:10.1186/1471-2164-11-179

Characterization of the ovine ribosomal protein SA gene and its pseudogenes

Broeke et al.,
1 Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium 2 Departamento de Mejora Genetica Animal, INIA, Ctra La Coruna Km 7.5, Madrid 28040, Spain

... Promoter sequences were searched with CISTER, Neural Network Promoter Prediction, FPROM and TFsearch [36,38-40]. ... 36. FGENESH Webserver [http://linux1.softberry.com] ...


Functional Plant Biology
2010 37, 194–205.

Cloning and characterisation of ZmZLP1, a gene encoding an endoplasmic reticulum-localised zinc transporter in Zea mays

Xu Y, Wang B, Yu J, Ao G, Zhao Q
A State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing 100193, China.

... The ZmZIP genomic sequences of Zea mays contigs were from http://maize.tigr.org/release5. 0/azm5.shtmL and were annotated for open reading frames using the gene prediction algorithms of FGenesH (http://www.softberry.com); the others are in GenBank (http://www.ncbi.nlm ...


PLoS Biol
2010, vol. 8, num. 2, e1000313

Genome sequence of the pea aphid Acyrthosiphon pisum

Rozas Liras et al.,

... 2007-04628 award to ACCW. FgenesH models were donated by Softberry, Inc. This research was additionally supported in part by the Intramural Research Program of the NIH, National Library of Medicine. The funders had no ...


BMC Plant Biology
2010, 10:246

Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

Gonzalez et al.,
Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain

... setting the minimum identity parameter to 92. In some cases, the FGENESH annotation software at http://linux1.softberry.com/berry.phtml, with Arabidopsis as plant model, was used to complement or improve the Augustus annotation. The predicted coding ... 


Plant Physiology
152:1772-1786 (2010)

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

Kamenetzky et al.,
Instituto de Biotecnologia, Instituto Nacional de Tecnologia Agropecuaria, and Consejo Nacional de Investigaciones Cientificas y Tecnicas, B1712WAA Castelar, Argentina (L.K., R.A., S.B., F.C.); Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo 05508–900, Brazil (F.d.G., L.B., M.-A.V.S., M.R.)

... S. pennellii BAC/cosmid full-length sequences as well as three S. lycopersicum BAC clones, C04HBa0331L22, C07HBa0061J13, and C11HBa0062I24, were annotated using two different gene prediction programs: FGENESH (www.softberry.com; Salamov and Solovyev, 2000 ... 


PLoS Pathog
2010 6(4): e1000846. doi:10.1371/journal.ppat.1000846

SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis

Gauthier et al.,
1 Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America, 2 Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America

... blast.ncbi.nlm.nih.gov/Blast.cgi). FGENESH was used to identify predicted exons and introns in the SREB gene (www.softberry.com). Generation of null mutants. Two vectors, pBTS4-KO1 and pBTS4-KO2, were used to delete. 


Mol Genet Genomics.
2010 Feb;283(2):135-45. Epub 2009 Dec 19

Genome-wide discovery of DNA polymorphism in Brassica rapa

Park S, Yu HJ, Mun JH, Lee SC.
Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Suwon, 441-440, Republic of Korea.

. 2009). A list of BAC clones with GenBank accession numbers is provided in Table S1. Ab initio gene prediction for the BAC sequences was obtained by using the FGENESH program (www.softberry.com) based on a B. rapa matrix. ... 


Developmental & Comparative Immunology
Volume 34, Issue 4, April 2010, Pages 465-473 doi:10.1016/j.dci.2009.12.007

In search of the origin of FREPs: Characterization of Aplysia californica fibrinogen-related proteins

A.M. Gorbushin, Y.V. Panchin, and N.V. Iakovleva
Institute of Evolutionary Biochemistry and Physiology RAS, pr. Torez 44, Saint-Petersburg 194223, Russia

... contigs having even weak similarity to juxtaposed IgSF and FreD domains were retrieved from the nucleotide database and the coding region was preliminary identified by several invertebrate gene prediction models using FGeneSH software (http://linux1.softberry.com/berry ...


Microbiology
156 (2010), 278-286; DOI 10.1099/mic.0.033886-0

A tyrosine O-prenyltransferase catalyses the first pathway-specific step in the biosynthesis of sirodesmin PL

Anika Kremer and Shu-Ming Li
Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany

... Computer-assisted sequence analysis. FGENESH (SoftBerry; http://linux1.softberry.com/) and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used for exon/intron prediction and sequence analysis, respectively. ... 


FGENESH 2009

Genome Biology and Evolution
2009 Vol. 1 265-277; doi:10.1093/gbe/evp025

Origin and Diversification of Land Plant CC-Type Glutaredoxins

M. Ziemann*, M. Bhave* and S. Zachgo**
*Environment and Biotechnology Centre, Faculty of Life and Social SciencesSwinburne University of Technology, Hawthorn, Victoria, Australia **Department of Botany, University of Osnabruck, Osnabruck, Germany

... gene models. In cases of low conservation of exon sequences and lack of transcript information, FGENESH hidden Markov model-based gene structure prediction (http://linux1.softberry.com/berry.phtml) was utilized. Values ...


Current Genetics
Volume 55, Number 3 / June, 2009 pp. 253-262

The telomere-linked helicase (TLH) gene family in Magnaporthe oryzae: revised gene structure reveals a novel TLH-specific protein motif

Cathryn J. Rehmeyer, Weixi Li, Motoaki Kusaba and Mark L. Farman
(1) Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA (2) Department of Biology, University of Kentucky, Lexington, KY 40546, USA

... Dean et al. 2005). The masked sequences were then used for gene prediction with Fgenesh (Salamov and Solovyev 2000) trained on M. oryzae sequences (Softberry, http://www.softberry.com). Various gene prediction tools ...


Nature
461, 1135-1138 (22 October 2009) | doi:10.1038/nature08498

A transposon-induced epigenetic change leads to sex determination in melon

Martin et al.,
(1) INRA-CNRS, UMR1165, Unite de Recherche en Genomique Vegetale, 2 rue Gaston Cremieux, F-91057 Evry, France (2) Plateforme de Cytologie et d’Imagerie Vegetale, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France

... After assembly, two forms of gene annotation were performed: (1) ab initio gene prediction with GENSCAN (http://genes.mit.edu/GENSCAN.html), GeneMark.hmm (http://exon.gatech.edu/ GeneMark/eukhmm.cgi) and FGENESH (http://www.softberry.com/berry.phtml); and (2 ...


Journal of Equine Veterinary Science
2009 Volume 29, Issue 6, Pages 519-526

Search for Polymorphism in Exon 2 of the Equine Leptin Gene

N. Huff, D. Thompson Jr., K. Bondioli

... View Within Article. Splicing donor and acceptor consensus sequences were located at the putative exon/intron borders. The predicted splice sites at the intron/exon boundaries were analyzed using a computer program (FGeneSH, Softberry, Inc., Mount Kisco, NY). ...


Molecular Genetics and Genomics
Volume 282, Number 2 / August, 2009, pp. 205-215

Genome-wide analysis of conservation and divergence of microsatellites in rice

Manish Roorkiwal 1, Atul Grover 1 and Prakash C. Sharma 1
(1) University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, 110403, India

.. 1.6.2 (Softberry; downloadable from http://www.molquest.com) prior to the alignment. This allowed much higher number of queries to be handled per day compared to a maximum of 25 per day when FGENESH was accessed through World Wide Web portal of Softberry. ...


Russian Journal of Plant Physiology
Volume 56, Number 4 / July, 2009, pp.532-539

Delimitation of the fgr gene for rice fragrance to a 28-kb DNA fragment

Ding et al.,
(1) College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100094, China (2) High-Tech Research Center, Shandong Academy of Agricultural Science, Jinan, Shandong, 250100, China

... region. The sequence analysis of this fragment using FGENESH (http:/www.softberry. com) predicted three candidate genes encoding putative 3-methyllcrotonyl- CoA carboxylase, putative isoleucyl-tRNA synthetase, and BADH2. ...


BMC Evolutionary Biology
2009, 9:271 doi:10.1186/1471-2148-9-271

The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks

Jing Wang et al.,
1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China and 2Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK

... Sequence analysis The coding sequences and amino acids ofBnFT paralogues were predicted using the software "Softberry FGENESH" online service (http://linux1.softberry.com/berry.phtml). ... "Softberry NSITE-PL" online service (http://linux1.softberry.com/berry.phtml). ...


Theor Appl Genet.
2009 May;118(8):1509-17. Epub 2009 Mar 6.

Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa)

Liu T, Mao D, Zhang S, Xu C, Xing Y.
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China.

... Putative ORF prediction in 107 kb region The putative open reading frame (ORF) in the 107-kb region was predicted by the online software FGENESH on the basis of the gene structure available on the Internet (http://linux1.softberry.com/berry.phtml?topic=fgenesh& ... Cited by 1 - Related articles - All 3 versions


PLoS One.
2009; 4(9): e6981 doi: 10.1371/journal.pone.0006981.

Identifying and Characterizing a Novel Protein Kinase STK35L1 and Deciphering Its Orthologs and Close-Homologs in Vertebrates

Pankaj Goyal, 1* Antje Behring, 1 Abhishek Kumar, 2 and Wolfgang Siess 1
1Institute for Prevention of Cardiovascular Diseases, University of Munich, Munich, Germany 2University of Bielefeld, Bielefeld, Germany

... This region was highly conserved among mammals (Figure 3B Figure 3 ). We investigated this region for coding sequences manually and by using different gene prediction software such as FGENESH (www.softberry.com). ...


Molecular Immunology
Volume 46, Issues 8-9, May 2009, Pages 1679-1687

The immunoglobulin heavy chain locus in the reptile Anolis carolinensis

Francisco Gambon Deza, Christian Sanchez Espinel and Susana Magadan Mompo
aUnidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n°, Vigo 36210, Pontevedra, Spain bInstituto Superior de Saude do Alto Ave (ISAVE), Quinta de Matos, Geraz do Minho, 4830-31 PVL, Portugal

... The constant region genes and exons were obtained by comparison with those already described for E. macularius. A dotplot was made with E. macularius and A. carolinensis sequences using the DNASTAR (lasergene), FGENESH and FEX software (http://www.softberry.com). ...


The Plant Genome
doi: 10.3835/?plantgenome.2009.01.0001 vol. 2 no. 3 211-223

Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution

Bindu Joseph et al.,
Dep. of Agronomy, Iowa State Univ., Ames, IA 50011

... (2006). BAC Sequence Analysis. The LG I UBP12 region BAC sequences were annotated using gene prediction programs FGENESH (www.softberry.com) and GeneMark (Lomsadze et al., 2005, http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi; verified 30 July 2009). ...


Plant Science
Volume 176, Issue 3, March 2009, Pages 352-359

Characterization of six novel NAC genes and their responses to abiotic stresses in Gossypium hirsutum L.

Chaomin Meng, Caiping Cai, Tianzhen Zhang and Wangzhen Guo
National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China

... Additionally, assembled sequences were compared to exon predictions from FGENESH (http://www.softberry.com). From these gene predictions, gene-specific primers (Table 1) were designed for PCR from cDNA and genomic DNA. ...


J Biosci.
2009 Jun;34(2):251-61.

Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice.

Ghazi IA, Srivastava PS, Dalal V, Gaikwad K, Singh AK, Sharma TR, Singh NK, Mohapatra T.
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110 012, India.

... The FASTA form of each BAC/PAC clone sequence was downloaded as a text file one by one. Gene prediction was performed for each clone using FGENESH (www. softberry.com) trained for monocot species (Salamov and Solovyer 2000). ...


TAG Theoretical and Applied Genetics
Volume 118, Number 6 / April 2009 pp. 1027-1034

Identification and mapping of Pi41 , a major gene conferring resistance to rice blast in the Oryza sativa subsp. indica reference cultivar, 93-11

Qinzhong Yang 1, 2, Fei Lin 1, Ling Wang 1 and Qinghua Pan 1
Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, 510642 Guangzhou, China

... markers. Flanking markers were used to identify candidate NBS- LRR genes, with the help of GENSCAN (http://genes.mit. edu), FGENSH (http://sun1.softberry.com) and RiceGAAS (http://rgp.dna.affrc.go.jp) software. The sequence ...


Developmental & Comparative Immunology
Volume 33, Issue 4, April 2009, Pages 547-558

Identification of an Atlantic salmon IFN multigene cluster encoding three IFN subtypes with very different expression properties

Baojian Sun, Borre Robertsen, Zhiqiang Wang and Bin Liu
aDepartment of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromso, N-9037 Tromso, Norway bInstitute of Oceanology, Chinese Academy of Sciences, Qingdao and Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

... 2.2. Bioinformatics. Annotation of genes in genomic sequences was performed by analysis with the programs Genscan (http://genes.mit.edu/GENSCAN.html) and Fgenesh (http://softberry.com) combined with manual inspections. ...


The Plant Genome
doi: 10.3835/?plantgenome2008.09.0007 vol. 2 no. 1 93-101

Gene Content and Distribution in the Nuclear Genome of Fragaria vesca

Pontaroli et al.,
Dep. of Genetics, Univ. of Georgia, Athens, GA 30602;

... Gordon et al., 1998). Fosmid Sequence Annotation. Ab initio gene prediction was performed on each fosmid sequence using FGENESH (Softberry, Inc., Mount Kisco, NY) with the Arabidopsis training set. All the obtained predicted ...


Planta
Volume 229, Number 4 / March, 2009, pp. 885-897

Regulation of the cellulose synthase-like gene family by light in the maize mesocotyl

Harrie van Erp 1, 2 and Jonathan D. Walton 1
(1) Department of Energy-Plant Research Laboratory, Michigan State University, E. Lansing, MI 48824, USA (2) Present address: Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA

... Supplementary Table S1). Proteins encoded by the MAGI sequences were determined using the FGENESH monocotyledon ab initio gene prediction program (http://www.softberry.com) (Yao et al. 2005). The predicted protein ...


BMC Plant Biol.
2009 Jul 17;9:93.

Identification of three wheat globulin genes by screening a Triticum aestivum BAC genomic library with cDNA from a diabetes-associated globulin.

Loit E, Melnyk CW, MacFarlane AJ, Scott FW, Altosaar I.
Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.

... sequence of Glo-3A were analyzed to identify a potential promoter using TSSP, a plant promoter recognition program (www.softberry.com) and PlantProm database [24]. A ... (http://www.ncbi.nih. gov/gorf/gorf.html) and FGENESH 3.0 alpha (www.softberry.com) ...


Plant Molecular Biology
Volume 70, Numbers 1-2 / May, 2009, pp. 47-61

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

Naxin Huo et al.,
(1) Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA (2) Department of Plant Sciences, University of California, Davis, CA 95616, USA

... In addition, coding regions in the BAC sequences were also predicted using FGENESH (http:// www.softberry.com) set for a monocot model. Predicted genes were then compared to the nonredundant and dbEST databases of NCBI (March 2008) using BLASTN and BLASTX. ...


Molecular Plant
2009 doi:10.1093/mp/ssp064

The CELLULOSE-SYNTHASE LIKE C (CSLC) Family of Barley Includes Members that Are Integral Membrane Proteins Targeted to the Plasma Membrane

Dwivany et al.,
Plant Cell Biology Research Centre, School of Botany, University of Melbourne Victoria 3010, Australia

... the 5' and 3' directions. Most of the intron/exon boundaries predicted by FGENESH (www.softberry.com) in the HvCSLC1 and HvCSLC4 genomic sequences were confirmed from EST data. A schematic representation of the ...


Plant Physiology and Biochemistry
Volume 47, Issue 7, July 2009, Pages 650-652

Evidence of a sirtuin gene family in grapevine (Vitis vinifera L.)

Matteo Busconi, Serena Reggi, Corrado Fogher and Luigi Bavaresco
aIstituto di Botanica e Genetica vegetale, Universita Cattolica del Sacro Cuore, Via Emilia Parmense, 84 29100 Piacenza, Italy bIstituto di Frutti-Viticoltura, Universita Cattolica del Sacro Cuore, Via Emilia Parmense, 84 29100 Piacenza, Italy

... When appropriate, the prediction of hypothetical gene structure was performed using the following software in parallel: FGENESH (http://linux1.softberry.com), GeneMark (http://exon.gatech.edu), and GENSCAN (http://genes.mit.edu). ...


Fungal Genetics and Biology
Volume 46, Issue 9, September 2009, Pages 695-706

Mutations to LmIFRD affect cell wall integrity, development and pathogenicity of the ascomycete Leptosphaeria maculans

Angela P. Van de Wouw, Filomena A. Pettolino, Barbara J. Howlett and Candace E. Elliott
aSchool of Botany, The University of Melbourne, Vic. 3010, Australia

... study are listed in Table 1. The coding region of a gene flanking the T-DNA insertion (subsequently referred to as LmIFRD) and a gene downstream of the T-DNA (subsequently referred to as LmcABH-like) were predicted using FGENESH software (http://www.softberry.com/berry ...


BMC Evol Biol.
2009 Jul 19;9:168.

Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloe festucae

Bryant MK, Schardl CL, Hesse U, Scott B.
Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand

... reading frames for SLP and unlinked non-SLP genes were identified using FGENESH, an HMM-based gene structural prediction using the Fusarium graminearum parameters (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfi nd). ...


Functional & Integrative Genomics
Volume 9, Number 1 / February, 2009, pp. 97-108

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Beng-Kah Song et al.,
(1) School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia (2) Genome Dynamics Program, Scottish Crop Research Institute, Dundee, DD2 5DA, UK

... affrc.go.jp/usr-bin/login.cgi) and was aided by the rice training set of the gene-finding program GeneMark.hmm (Lukashin and Borodovsky 1998, http://genemark.biology. gatech.edu/GeneMark/), fgenesh (http://www.softberry. com/berry.phtml) and RiceHMM (Sakata et al. ...


Genetics
Published Articles Ahead of Print: October 12, 2009, doi:10.1534/genetics.109.106922

Fine Mapping and Haplotype Structure Analysis of a Major Flowering Time Quantitative Trait Locus on Maize Chromosome 10

Ducrocq et al.,
INRA

... c0111K09) were analyzed using TE-Nest (KRONMILLER and WISE 2008) and RepeatMasker (http://www.repeatmasker.org/) in order to localize transposable elements. Masked sequences were annotated using Fgenesh (http://linux1.softberry.com/berry.phtml, version 2.6). ...


Plant Molecular Biology Reporter
Volume 27, Number 4 / December, 2009, pp. 526-533

The Promoters of Forisome Genes MtSEO2 and MtSEO3 Direct Gene Expression to Immature Sieve Elements in Medicago truncatula and Nicotiana tabacum

Noll et al.,
1) Institut fur Biochemie und Biotechnologie der Pflanzen der Westfalischen Wilhelms, Universitat Munster, Hindenburgplatz 55, Munster, 48143, Germany (2) Department of Biology, University of York, Heslington, York, YO10 5DD, UK

... The MtSEO promoter sequences were aligned using the Lasergene software package v7.1 (DNAstar, Madison, WI, USA). Putative TATA box sequences were identified by analyzing the corresponding genomic clone using the FGENESH program (http://www.softberry.com). ...


Molecular Genetics and Genomics
Volume 281, Number 5 / May, 2009, pp. 565-578

Characterization of cyclophilin-encoding genes in Phytophthora

Pamela Hui Peng Gan 1 , Weixing Shan 1, 2, Leila M. Blackman 1 and Adrienne R. Hardham 1
1) Plant Cell Biology Group, Research School of Biological Sciences, School of Biology, The Australian National University, GPO Box 475, Canberra, ACT, 2601, Australia (2) Present address: College of Plant Protection, Northwest A & F University, Yangling, China

... eng/scripts/01_13.html. Genes were predicted from genomic sequences using FGENESH (Softberry Inc., Mount Kisco, NY, USA), with diatom-speciWc parameters and GENSCAN (Chesnick et al. 2000). To analyze pro- moter ...


Heredity.
2009 Mar;102(3):266-73. Epub 2008 Nov 12

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

Jang et al.,
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.

... GAP2 (Huang, 1994) programs. Alternatively, gene structures were predicted by FGE- NESH gene prediction software (http://sun1.softberry. com/berry.phtml) with the training set for monocot plants. Orthologs of Oryza sativa ...


Molecular Breeding
Volume 24, Number 4 / November, 2009, pp. 433-446

Development of SNP markers linked to the L locus in Capsicum spp. by a comparative genetic analysis

Hee-Bum Yang 1, Wing Yee Liu 1, Won-Hee Kang 1, Molly Jahn 2 and Byoung-Cheorl Kang
(1) Department of Plant Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul, 151-921, Korea (2) College of Agriculture and Life Science, University of Wisconsin, Madison, WI 53706, USA

... National University, Korea). BAC sequence annotation The FGENESH program (http://linux1.softberry.com/ berry.phtml) was used to predict genes from the contig sequence based on tomato organism informa- tion. To search for ...


BMC Biol.
2009 Jul 23;7:43.

Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes

Hui et al.,
Department of Zoology, University of Oxford, Oxford, UK

... To find additional genes in these contigs besides the ParaHox genes, the entire contig sequences were scanned with GENSCAN and FGENESH (implemented at www.softberry.com [79]), and all predicted peptide sequences searched against Genbank with BLASTP. ...


Genetics
Vol. 181, 405-419, February 2009, doi:10.1534/genetics.108.093583

Molecular Analysis of a Large Subtelomeric Nucleotide-Binding-Site–Leucine-Rich-Repeat Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris

Geffroy et al.,
* Institut de Biotechnologie des Plantes, UMR-CNRS 8618, INRA, Universite Paris-Sud, 91 405 Orsay, France, Department of Chromosome Biology, University of Vienna, 1030 Vienna, Austria

... Ann Arbor, MI). The genomic sequence was annotated by using the gene prediction program Fgenesh (Softberry website) and was manually edited by a homology search against available databases. The genomic sequence ...


Molecular Biology and Evolution
2009 26(7):1651-1661; doi:10.1093/molbev/msp076

Sixty Million Years in Evolution of Soft Grain Trait in Grasses: Emergence of the Softness Locus in the Common Ancestor of Pooideae and Ehrhartoideae, after their Divergence from Panicoideae

Charles et al.,
* Unite de Recherches en Genomique Vegetale (UMR INRA 1165–CNRS 8114UEVE), Organization and evolution of Plant Genomes, Evry, France Plant Genome Mapping Laboratory, University of Georgia

... We used the gene prediction given by the program FGENESH (http://www.softberry.com; with the Monocot matrix) as well as BlastN and BlastX and TBlastX alignments against dbEST (http://www.ncbi.nlm.nih.gov/), SwissProt (http://expasy.org/sprot/), and synteny with ...


BMC Genomics.
2009 Aug 13;10:376.

Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

O'Rourke et al.,
Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USA.

... QTL (Figure 1, Additional files 1 and 2). Sequences of the delineated iron QTL regions were analyzed using FGENESH (www.softberry.com) using Arabidopsis as the training model to identify gene structure predictions. The ...


Fungal Genetics and Biology
Volume 46, Issue 5, May 2009, Pages 353-364

Biosynthesis of the cyclooligomer depsipeptide bassianolide, an insecticidal virulence factor of Beauveria bassiana

Yuquan Xu et al.,
aSW Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706-6800, USA bDepartment of Entomology, College of Agriculture and Life Sciences, The University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, USA

... closure. Sequence assembly was done with Sequencher 4.7 (Gene Codes Corp). HMM-based gene models were built with FGENESH (Softberry) using the F. graminearum and the Aspergillus nidulans training sets. The models ...


Theor Appl Genet.
2009 Apr;118(6):1199-209. Epub 2009 Feb 15.

ps-2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene

Gorguet B, Schipper D, van Lammeren A, Visser RG, van Heusden AW.
Graduate School of Experimental Plant Sciences, Wageningen UR Plant Breeding, PO Box 386, 6700 AJ, Wageningen, The Netherlands

... genetic map. ORF4, a putative polygalacturonase gene, mapped the clos- est to the ps-2 locus (Fig. 2). Subsequently, the putative introns and exons were identiWed using the FGENSH soft- ware of Softberry. The candidate ...


Molecular & Cellular Proteomics
October 1, 2009, 8, 2368-2381.

In Planta Proteomics and Proteogenomics of the Biotrophic Barley Fungal Pathogen Blumeria graminis f. sp. hordei

Bindschedler et al.,
School of Biological Sciences, The University of Reading, P. O. Box 221, Reading RG6 6AS, United Kingdom, Centre for Bioinformatics, Imperial College, Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom

... to predict ORFs. Putative ORFs were determined with the FGENESH prediction program using either the Leptosphaeria maculans or the Sclerotinia sclerotiorum ORF prediction models (SoftBerry, Inc.). Putative classical secretion ...


PLoS Pathog.
2009 January; 5(1): e1000261.

Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi

Akiyoshi et al.,
1Division of Infectious Diseases, Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America 2Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America

... ECU08_1090/ECU08_1100). Introns. DNA sequences of contigs greater than 10 kb were analyzed by FGENESH (http://www.softberry.com; [44]), an HMM-based gene structure prediction program, to identify putative introns. For the ... Cited by 11 - Related articles - All 7 versions


BMC Res Notes.
2009; 2: 206.

Intragenic tandem repeats in Daphnia magna: structure, function and distribution

Isabelle Colson,1 Louis Du Pasquier,1 and Dieter Ebert 1
1Basel University, Zoological Institute, Vesalgasse 1, CH-4051 Basel, Switzerland

... 18. Salamov A, Solovyev V:Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000,10: 516-522. 19. Fgenesh [http://linux1.softberry.com/berry.phtml?topic= fgenesh&group=programs&sy bgroup=gfind]. Page 13. - 12 - 20. ...


World Journal of Microbiology and Biotechnology
Volume 25, Number 6 / June, 2009, pp. 989-995

Characteristic analysis of transformants in T-DNA mutation library of Monascus ruber

Shao et al.,
(1) College of Food Science and Technology, Huazhong Agricultural University, Hongshan District, 430070 Wuhan, Hubei, People’s Republic of China

... et al. 2004) was carried out to extend the DNA sequences flanking TAIL-PCR products. Up to now, we have amplified eight full DNA sequences, which were submitted to FGENESH (http://linux1.softberry.com/berry. phtml) to ...


PLoS Pathogens
January 2009, Volume 5, Issue 1, e1000261. doi:10.1371/journal.ppat.1000261

Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi

Akiyoshi et al.,
1 Division of Infectious Diseases, Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America, 2 Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America

... ECU08_1090/ECU08_1100). Introns. DNA sequences of contigs greater than 10 kb were analyzed by FGENESH (http://www.softberry.com; [44]), an HMM-based gene structure prediction program, to identify putative introns. For the ...


PNAS
February 17, 2009 vol. 106 no. 7 2295-2300 doi: 10.1073/pnas.0807350106

Duplicate genes increase expression diversity in closely related species and allopolyploids

Misook Ha a,b,c, Eun-Deok Kim a and Z. Jeffrey Chen a,b,c,d
Sections of aMolecular Cell and Developmental Biology and dIntegrative Biology bCenter for Computational Biology and Bioinformatics, and cInstitute for Cellular and Molecular BiologyOne University StationA-4800University of TexasAustinTX 78712

... The sequencing reads were assembled and edited. A. arenosa genes were annotated using FGENESH (www.softberry.com) and BLAST against cDNA sequences of A. thaliana. Annotated genomic sequences are deposited in GenBank (accession no. FJ461780). ...


Plant Physiology
149:286-296 (2009)

A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice

Manosalva et al.,
Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, Colorado 80523–1177 (P.M.M., R.M.D, J.E.L.); Plant Pathology, Kansas State University, Manhattan, Kansas 66502–5502 (P.M.M.);

... cgi) using the HTGS database. FGENESH (http://www.softberry.com/berry.phtml) was used to predict putative oxalate oxidase and OsGLP from significant rice bacterial artificial chromosome hits. All nucleotide and inferred amino ...


Plant Journal.
60(1):181-193, October 2009.

Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider

Jiang N, Gao D, Xiao H, van der Knaap E.
Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.

... Tomato eIF4a6 was used to assess equal loading and mRNA and cDNA quality. Primer sequences are listed in Table S3. Annotations TOP. The gene sequences were identified using the ab initio gene prediction program FGENESH (http://www.softberry.com/berry.phtml ). ...


Nucleic Acids Research
2009, Vol. 37, Database issue D750-D754 doi:10.1093/nar/gkn887

SpBase: the sea urchin genome database and web site

R. Andrew Cameron, Manoj Samanta, Autumn Yuan, Dong He and Eric Davidson
Center for Computational Regulatory Genomics, Beckman Institute 139–74, California Institute of Technology, Pasadena, CA 91104, USA

... were independently employed by individual groups to arrive at sets of gene models for eventual annotation: Gnomon at NCBI (13); FgenesH from Softberry (14,15 ...


FGENESH 2008

Nature
2008, 4doi:10.1038/nature07410

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Bowler et al.
1. CNRS UMR8186, Department of Biology, Ecole Normale Supe'rieure, 46 rue d'Ulm, 75005 Paris, France
2. Stazione Zoologica 'Anton Dohrn', Villa Comunale, I-80121 Naples, Italy

... Gene predictors used for these annotations included ab initio Fgenesh 12 trained on sets of known genes and reliable homology-based gene models from P. tricornutum and T.pseudonana, and homology-based Fgenesh+ 12 and Genewise 13 seeded by BLASTX alignments against sequences in the NCBI non-redundant protein set. ...


Nature
2008, 452, 949 - 955.

The genome of the model beetle and pest Tribolium castaneum.

Richards et al.
1. Human Genome Sequencing Cente
2. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

... Work at the BCM-HGSC was funded by grants from the NHGRI and USDA. FgenesH and FgenesH++ analysis was donated by Softberry Inc. This research was additionally supported in part by the Intramural...


Nature
2008, 452, 991 - 996.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Ming et al.
Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

...in training ab initio gene prediction software Augustus, GlimmerHMM and SNAP. Ab initio gene prediction software Fgenesh, Genscan and TWINSCAN were trained on Arabidopsis. Spliced alignments of proteins from the plant division of...


Nature
Volume 453 Number 7198 pp1064 - 1071 (19 Jun 2008), doi: 10.1038/nature06967

The amphioxus genome and the evolution of the chordate karyotype.

Putnam et al.
# Department of Energy Joint Genome Institute, Walnut Creek California 94598, USA
# Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

... A\Supplementary Note 3. Annotation of protein coding genes 3.1 Expressed sequence tag sequencing. cDNA libraries for amphioxus were prepared from gastrula and neurula stage embryos, and from larvae as described by 6, and a single library was created for Petromyzon marinus (sea lamprey). Approximately 32,000 expressed sequence tags (ESTs) were attempted from each library. (Supplementary Table S6). 3.2 Gene prediction, functional annotation and quality control. The JGI Annotation Pipeline was used for annotation of the amphioxus v1.0 assembly described here. The pipeline includes the following steps: (1) repeat masking, (2) mapping ESTs, full length cDNAs, and putative full length known genes, (3) gene structure prediction using several methods, (4) protein functional annotation using several methods, and (5) combining gene predictions into a non redundant representative set of gene models, which are subject to genome-scale analysis. The genomic sequence, predicted genes and annotations of amphioxus, together with available evidence, are available at the JGI Genome Portal (www.jgi.doe.gov/Amphioxus) and from GenBank under accession number ABEP01000000. Transposons were masked using RepeatMasker 7 tools and a custom library of manually curated repeats (see above Supplementary Note 2.4). 480,070 ESTs were clustered into 77,402 consensus sequences and both individual ESTs and consensus sequences were mapped onto genome assembly using BLAT4. Gene predictors used for annotation of amphioxus v1.0 included ab initio FGENESH 8, homology- based FGENESH+ 8, homology-based GENEWISE 9, and EST-based ESTEXT (Grigoriev, unpublished, available upon request). ...


Nature
452, 88 - 92 (06 Mar 2008), doi: 10.1038/nature06556, Letter

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Martin et al.,
MR 1136, INRA-Nancy Universite, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.

...in the scaffold assembly (Supplementary Table 2). Genome annotation Gene models were predicted using FgenesH, homology-based FgenesH+ (ref. 18) and Genewise, as well as EuGAne and TwinScan, and alignments of several complementary DNA...


Nature
451, 193 - 196 (10 Jan 2008), doi: 10.1038/nature06453, Letter

Identification of the sex genes in an early diverged fungus

Alexander Idnurm, Felicia J. Walton, Anna Floyd, Joseph Heitman
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.

...were searched with BLASTp, BLASTn or tBLASTn programs. Gene predictions from unannotated genomic DNA were made with FGENESH software using the settings for Schizosaccharomyces pombe. HMG domains were aligned in ClustalW, in MacClade...


Genetics
Published Articles Ahead of Print: December 15, 2008, doi:10.1534/genetics.108.093583

Molecular Analysis of a Large Subtelomeric NBS-LRR Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris

Valerie et al.,
Institut de Biotechnologie des Plantes University of Vienna Institut Pasteur

... Arbor, MI, USA). The genomic sequence was annotated by using the gene prediction program Fgenesh (Softberry website) and was manually ...


PLoS Genet.
2008 November; 4(11): e1000261.

Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism

Erik C. Madsen and Jonathan D. Gitlin
Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America

... This contig was scanned for potential genes using the FGENESH program (www.softberry. com) and comparing to the Ensembl database (www.ensembl.org). ...


BMC Plant Biology
2008, 8:133 doi:10.1186/1471-2229-8-133

The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula

Shin et al.,
Department of Plant Science, Seoul National University, Seoul 151-921, Korea

... FgeneSH on an Arabidopsis matrix, because the resultswere better suited for BLASTZ resultsthan that of the Medicago matrix (http://www.softberry.com). Each ...


BMC Genomics
2008, 9:555 doi:10.1186/1471-2164-9-555

New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides

Salse et al.,
Organisation and Evolution of Plant Genomes (OEPG), UMR INRA 1165 - CNRS 8114 UEVE - Unite de Recherche en Genomique Vegetale (URGV). 2, rue Gaston Cremieux, CP5708, 91057 Evry cedex. France.

Gene structures and putative functions were identified by combining results of BLASTN and BLASTX alignments against dbEST (http://www.ncbi.nlm.nih.gov/) and SwissProt databases (http://expasy.org/sprot/), with results of 2 gene predictor programs, Page 17 15 Eugene [53] with rice (Oryza sativa) training version and FgeneSH [54] (with default parameters (http://sun1.softberry.com/).


BMC Genetics
2008, 9:78 doi:10.1186/1471-2156-9-78

Genomic Complexity of the Variable Region-Containing Chitin-Binding Proteins in Amphioxus

Dishaw et al.,
All Children’s Hospital,Department of Molecular Genetics,801SixthStreet South,St. Petersburg,FL 33701,USA

... html),FGENESH and FGENESH+ (http://linux1.softberry.com/all.htm) or genomescan[63,66] (http://genes.mit.edu/genomescan. html).Details ...


BMC Evolutionary Biology
2008, 8:115 doi:10.1186/1471-2148-8-115

Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins

Michal Grunt, Viktor Zarsky and Fatima Cvrckova
Department of Plant Physiology, Faculty of Sciences, Charles University, Vinicna' 5, CZ 128 43 Praha 2, Czech Republic

... For each new gene, splice sites were predicted using at least three of the following eukaryotic gene-prediction programs: GeneMark.hmm [84], FGENESH [85] at the Softberry, Inc. website [86] ...


Appl. Environ. Microbiol.
December 2008 doi:10.1128/AEM.01889-08

Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus

Gumer Perez, Jasmyn Pangilinan, Antonio G. Pisabarro, and Lucia Ramirez
Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain; DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

... The Hidden 153 Markov Model (HMM)-based program FGENESH was used for web-based gene 154 prediction (http://www.softberry.com/berry.phtml). ...


International Journal of Integrative Biology
2008 v.3 No 1, 50

SNP in Granule Bound Starch Synthase-I (GBSS-I) gene in Indian rice genotypes

SK Srivastava, U Roy

... The genes for both the BACs have been predicted using FGENESH software (http://www.softberry.com), which revealed the presence of 23 and 34 genes respectively ...


International Journal of Plant Genomics
Volume 2008, Article ID 391259, 8 pages doi:10.1155/2008/391259

Conserved Microsynteny of NPR1 with Genes Encoding a Signal Calmodulin-Binding Protein and a CK1-Class Protein Kinase in Beta vulgaris and Two Other Eudicots

David Kuykendall, Jonathan Shao, and Tammy Murphy
Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Building 004, Room 120, Beltsville, MD 20705, USA

... The sequence contig was screened for coding sequence using a combination of the following programs: GeneMark [18, 19] for eukaryotes (http://exon.gatech.edu/GeneMark/eukhmm.cgi), GenScan (http://genes.mit.edu/GENSCAN.html), FGENESH (http:// softberry.com/), and GRAIL ...


BMC Genomics
2008, 9:563 doi:10.1186/1471-2164-9-563

The UDP-glucosyltransferase multigene family in Bombyx mori

Huang et al.,
The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China

... query sequence and its flanking regions were extracted, and put into Softberry database for predicting new genes by using FGENESH taking the available insect...


CURRENT SCIENCE
VOL. 95, NO. 8, 25 OCTOBER 2008

Identification of candidate gene-based markers (SNPs and SSRs) in the zinc and iron transporter sequences of maize (Zea mays L.)

Arti Sharma and R. S. Chauhan
Advanced Centre of Hill Bioresources and Biotechnology, CSK HP Agricultural University, Palampur 176 062, India Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, P.O. Dumehar Bani, Kandaghat, Solan 173 215, India

... for open reading frames (ORFs), including the promoter regions and the 3?UTRs using gene prediction algorithms of FGenesH (http:// sun1.softberry.com/berry ...


Yeast
Sequencing Report 2008 Volume 25 Issue 9, Pages 673 - 679

The gap-filling sequence on the left arm of chromosome 2 in fission yeast Schizosaccharomyces pombe

Sasaki et al.,
ASPEX Division, Research Centre, Asahi Glass Co., Ltd., Japan

... Corporation). ORFs, introns and exons were predicted using FGENESH (http://www.softberry.com/) (Sala- mov et al., 2000) on an Sz. ...


Insect Biochemistry and Molecular Biology
Volume 38, Issue 12, December 2008, Pages 1111-1120

A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori

Chai et al.,
The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China

... The intergenic sequences where the lost homeobox genes were found were further put into the Softberry database for predicting new genes by using the FGENESH ...


International Journal of Integrative Biology
2008 Volume 2 N.3 pp.153-156

Sprome: A database on promoters of abiotic stress inducible genes in rice

R Sundheep, L Arul, P Nagarajan, P Balasubramanian

...FGENESH, a gene prediction tool based on Hidden Markov Model (HMM) was used to predict the presence of plausible Exon/UTR in the putative promoter region (http://www.softberry.com/berry ...


Trends in Biochemical Sciences
Volume 33, Issue 12, December 2008, Pages 577-582

Eukaryote polyphosphate kinases: is the 'Kornberg' complex ubiquitous?

Paul Hooley, Michael P. Whitehead and Michael R.W. Brown
School of Applied Sciences, Wulfruna Street, University of Wolverhampton, Wolverhampton, WV1 1SB, UK

... Genome projects perform automatic annotations using gene-finding programs such as FGENESH (Softberry) or Artemis (Sanger Centre), with somewhat arbitrary cut ...


Heredity
12 Nov 2008, doi: 10.1038/hdy.2008.119

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

C S Jang, T L Kamps, H Tang, J E Bowers, C Lemke, A H Paterson
1. 1Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA 2. 2Plant Genomics Lab, Department of Applied Plant Sciences Technology, Kangwon National University, Chuncheon, Korea

... Alternatively, gene structures were predicted by FGENESH gene prediction software (http://sun1.softberry.com/berry.phtml) with the training set for monocot plants. Orthologs of Oryza sativa corresponding to...


Theor Appl Genet
DOI 10.1007/s00122-008-0888-y

Fine genetic mapping of xa24, a recessive gene for resistance against Xanthomonas oryzae pv. oryzae in rice

Xiaoming Wu, Xianghua Li, Caiguo Xu and Shiping Wang
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

... Gene prediction analysis was performed with the programs GENSCAN (http://genes.mit. edu/GENSCAN.html), FGE- NESH (http://www.softberry.com/berry.phtml) and Gene ...


Gene
Volume 424, Issues 1-2, 15 November 2008, Pages 71-79 doi:10.1016/j.gene.2008.07.027

SRWD: A novel WD40 protein subfamily regulated by salt stress in rice (Oryzasativa L.)

Ji Huang et al.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China

... Using corresponding genomic sequence, the opening read frame (ORF) was predicted by Fgenesh program at Softberry server (http://www.softberry.com) and this ...


Molecular Plant
2008 1(5):830-838; doi:10.1093/mp/ssn045

Fine Mapping of Spr3, a Locus for Spreading Panicle from African Cultivated Rice (Oryza glaberrima Steud.)

Ji-Jing Luo, Wei Hao, Jian Jin, Ji-Ping Gao and Hong-Xuan Lin
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China

... The counterpart DNA sequences of the interval defined by the markers L4359 and L4264 of Nipponbare were predicted with FGENESH of Softberry (www.softberry.com ...


Genome
Volume 51, Number 6, 1 June 2008 , pp. 452-464(13)

Comparative genomic analysis of the whale (Pseudorca crassidens) PRNP locus

Kim, Dae-Won et al.

... Ab initio gene pre- diction was performed on the genomic sequences using FGENESH (SoftBerry, Inc., Mount Kisco, New York; http:// www.softberry.ru/berry.phtml ...


Fungal Genetics and Biology
Volume 45, Issue 11, November 2008, Pages 1487-1496 doi:10.1016/j.fgb.2008.08.009

Characterization of the atromentin biosynthesis genes and enzymes in the homobasidiomycete Tapinella panuoides

Patrick Schneider, Sarah Bouhired and Dirk Hoffmeister
Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universitat, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany

... The Aspergillus or Phanerochaete search algorithms of FGENESH (Softberry, Mount Kisco, NY) were used to predict gene structures and exon/intron junctions. 2.5. ...


Molecular Phylogenetics and Evolution
Volume 49, Issue 1, October 2008, Pages 349-355 doi:10.1016/j.ympev.2008.04.025

Molecular evolution and diversification of plant cysteine proteinase inhibitors: New insights after the poplar genome

M. Margis-Pinheiro et al.
a Programa de Pos-graduacao em Genetica e Biologia Molecular, Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Brazil
b Programa de Pos-graduacao em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Brazil
c Departamento de Bioquimica, Instituto de Ciencias Basicas da Saude, Universidade Federal do Rio Grande do Sul, Brazil

... Genomic sequences from Arabidopsis thaliana and Oryza sativa were also analyzed in the FGENESH gene structure prediction program (http://www.softberry.com/). ...


J. Biol. Chem.
Vol. 283, Issue 40, 26859-26868, October 3, 2008 doi:10.1074/jbc.M804979200

Ergot Alkaloid Biosynthesis in Aspergillus fumigatus:
OVERPRODUCTION AND BIOCHEMICAL CHARACTERIZATION OF A 4-DIMETHYLALLYLTRYPTOPHAN N-METHYLTRANSFERASE


Ole Rigbers and Shu-Ming Li
From the Heinrich-Heine-Universitat Dusseldorf, Institut fur Pharmazeutische Biologie und Biotechnologie, Universitatsstrasse 1, D-40225 Dusseldorf, Germany and the Philipps-Universitat Marburg, Institut fur Pharmazeutische Biologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany

... Computer-assisted Sequence Analysis-FGENESH (Softberry, Inc.) and the DNASIS software package (version 2.1; Hitachi Software Engineering, San Bruno, CA) were ...


Gene
Volume 418, Issues 1-2, 15 July 2008, Pages 41-48 doi:10.1016/j.gene.2008.04.005

Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?

V. E. Anisimova et al.
a Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117871 Moscow, Russia b Evrogen JSC, Miklukho-Maklaya 16/10, 117871 Moscow, Russia

... The putative N- and/or C-terminal terminal ends were searched in the genomic regions using FGENESH software (http://sun1.softberry.com). ...


Int J Plant Genomics
2008: 348621. Published online 2008 June 18. doi: 10.1155/2008/348621.

Development in Rice Genome Research Based on Accurate Genome Sequence

Takashi Matsumoto, Jianzhong Wu, Baltazar A. Antonio, and Takuji Sasaki
Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 3058602, Japan

... It retrieves rice sequences from GenBank and analyzes them with gene prediction programs such as Genscan [31] and FgeneSH (http://www.softberry.com/berry.phtml ...


Molecular Genetics and Genomics
Volume 279, Number 5 / May 2008 pp. 473-480

Construction of a fosmid library of cucumber ( Cucumis sativus ) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon ( Cucumis melo )

J. D. F. Meyer, W. Deleu3, J. Garcia-Mas and M. J. Havey
(1) Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
(2) Vegetable Crops Unit, Agricultural Research Service, US Department of Agriculture, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
(3) IRTA, Centre de Recerca en Agrigenomica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain

... 1997; http://www.ncbi.nlm.nih.gov/ BLAST/), GENESCAN (Burge and Karlin 1997; http:// www.genes.mit.edu/GENSCAN.html), and FGENESH (http://www.softberry.com). ...


Molecular Breeding
Volume 22, Number 4 / November 2008 pp. 593-602

Cloning and sequence diversity analysis of GmHs1 pro-1 in Chinese domesticated and wild soybeans

Cuiping Yuan et al.
(1) Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Crop Germplasm & Biotechnology, Ministry of Agriculture, Beijing, 100081, China
(2) Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China

... ORF and amino acid sequence were predicted with FGENESH 2.5 software (http://www. softberry.com) and used as a basis to estimate sequence diversity at ...


Genetics.
Published Articles Ahead of Print: September 9, 2008, doi:10.1534/genetics.108.092304

Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat

Mathieu Charles et al.
1 URGV (INRA-CNRS-UEVE), 2 CEA Genoscope, 3 Murdoch University, 4 INRA

... Six genes (of known or unknown function) and two putative genes were identified using the FGENESH prediction software (http://www.softberry. com) and by identification of homologs in rice (Figure ...


Gene
Volume 420, Issue 2, 1 September 2008, Pages 135-144 doi:10.1016/j.gene.2008.05.019

Expression analysis of rice A20/AN1-type zinc finger genes and characterization of ZFP177 that contributes to temperature stress tolerance

Ji Huang et al.
State key laboratory of crop genetics and germplasm enhancement, Nanjing Agricultural University, Nanjing 210095, China

... By database searching and FgeneSH prediction (http://www.softberry.com), it was found 12 putative proteins containing both A20 and AN1 zinc finger motifs in ...


Molecular Breeding
Volume 22, Number 4 / November 2008 pp. 603-612

Gene identification and allele-specific marker development for two allelic low phytic acid mutations in rice ( Oryza sativa L.)

Zhao et al.
(1) IAEA-Zhejiang University Collaborating Center, National Key Laboratory of Rice Biology and Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
(2) Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
(3) Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria

... et al. 2004). Gene prediction was made using the FGENESH program available on http://www.softberry.com/berry.phtml. PCR primers ...


Crop Sci
48:S-49-S-68 (2008)

Structural Features of the Endogenous CHS Silencing and Target Loci in the Soybean Genome

Jigyasa H. Tuteja and Lila O. Vodkin
Dep. of Crop Sciences, 384 ERML, 1201 W. Gregory Dr., Univ. of Illinois, Urbana, IL 61801.

... For ab initio predictions, FGeneSH with the Medicago truncatula-based training set (http://www.softberry.com; verified 9 Jan. 2008) was run. ...


Gene
Volume 411, Issues 1-2, 31 March 2008, Pages 27-37

Multiple tandem gene duplications in a neutral lipase gene cluster in Drosophila

Irene Horne and Victoria S. Haritos
CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia

... Genomic regions containing significant sequence similarity in multiple regions were then examined for genes using FGENESH on Softberry (http://www.softberry.com ...


J. Virol.
July 2008, p. 6697-6710, Vol. 82, No. 13 doi:10.1128/JVI.00212-08

A single Banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus (EPRV)

Philippe Gayral et al.,
CIRAD BIOS, UMR Biologie et Ge'ne'tique des Interactions Plante-Parasite (BGPI), TA 4-54/K Campus international de Baillarguet, F-34398 Montpellier Cedex 5, France;

... genes (FgenesH for monocot plants (44), softberry software (http://www.softberry. com) and 184 ACCEPTED at Google Indexer on May 20, 2008 jvi.asm.org ...


Int. J. Mol. Sci.
2008, 9, 1717-1729; DOI: 10.3390/ijms9091717

Are the Genes nadA and norB Involved in Formation of Aflatoxin G1

Kenneth C. Ehrlich, Leslie L. Scharfenstein Jr., Beverly G. Montalbano and Perng-Kuang Chang
Southern Regional Research Center, 1100 Robert E. Lee Blvd, P.O. Box 19687, New Orleans, LA 70179, USA

... a coding sequence with a single intron are predicted for nadA in A. parasiticus SU-1 and BN008 isolates based on an analysis using the Softberry FGENESH coding ...


New Phytologist
Volume 179 Issue 1 Page 196-208, July 2008

Magnaporthe grisea avirulence gene ACE1 belongs to an infection-specific gene cluster involved in secondary metabolism

Jerome Collemare et al.,
UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France

... FgenesH (http://www.softberry.com) was used to identify introns using Schizosaccharomyces pombe and Neurospora crassa matrices. ...


Chembiochem
Volume 9 Issue 7, Pages 1019 - 1023, 2008

Synthetic Strategy of Nonreducing Iterative Polyketide Synthases and the Origin of the "Classical Starter-Unit Effect"

Jason M. Crawford, Dr., Anna L. Vagstad, Karen P. Whitworth, Kenneth C. Ehrlich, Dr., Craig A. Townsend, Dr.
1Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, Fax: (+1) 410-516-8420 2Southern Regional Research Center, United States Department of Agriculture, 1100 RE Lee Boulevard, New Orleans, LA 70124, USA

... by using the revised sequence re- sulted in an alternative splicing pattern that translated through the GXCXG motif (FGENESH, http://www.softberry.com, Sup ...


Trends in Plant Science
doi:10.1016/j.tplants.2008.02.009

Diamonds in the rough: mRNA-like non-coding RNAs

Linda A. Rymarquis, James P. Kastenmayer, Alexander G. Huttenhofer and Pamela J. Green
Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA 213501 Hamlet Square Court, Germantown, MD 20874, USA 3Innsbruck Biocentre, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl Stra?e 3, 6020 Innsbruck, Austria

... The remaining RNAs are screened for ORFs, using programs such as GeneMark [25], GenScan [26], Fgenesh (www.softberry.com) or EST scan [27]. ...


Mycological Research
Volume 112, Issue 2, February 2008, Pages 216-224

Processing sites involved in intron splicing of Armillaria natural product genes

Mathias Misieka and Dirk Hoffmeister
Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universitat, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany

... For exon/intron identification we used the Aspergillus and Phanerochaete mode implemented in FGENESH (Softberry, Mount Kisco, NY) and Augustus (Stanke & ...


Current Bioinformatics
Volume 3, Number 2, May 2008 , pp. 87-97(11)

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

Foissac, Sylvain et al.,

... Simultaneously, a specific version of FGenesH was built for M. truncatula by the SoftBerry company (http://www.- softberry.com/). ...


Mol Biol Evol.
25(5):892-902; doi:10.1093/molbev/msn029

Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae

Norman Warthmann, Sandip Das, Christa Lanz and Detlef Weigel
Department of Molecular Biology, Genome Center, Max Planck Institute for Developmental Biology, D-72076 Tubingen, Germany

... 2005) and FGENESH (www.softberry.com) were used to predict putative novel ORFs, and validated using TBLASTN against the NCBI nr database. 6 Page 7. ...


FEMS Yeast Research
Volume 8 Issue 3 Page 432-441, May 2008

The endogenous adrenodoxin reductase-like flavoprotein arh1 supports heterologous cytochrome P450-dependent substrate conversions in Schizosaccharomyces pombe

Kerstin M. Ewen, Burkhard Schiffler, Heike Uhlmann-Schiffler, Rita Bernhardt, Frank Hannemann
Department of Biochemistry, Saarland University, Saarbrucken, Germany; and Department of Medical Biochemistry, Saarland University, Homburg, Germany

... The program fgenesh (http://www.softberry.com) was applied to identify the position and composition of the arh1 gene as well as to deduce the amino acid ...


Eukaryotic Cell
February 2008, p. 368-378, Vol. 7, No. 2

A Botrytis cinerea Emopamil Binding Domain Protein, Required for Full Virulence, Belongs to a Eukaryotic Superfamily Which Has Expanded in Euascomycetes

A. Gioti et al.,
UMR1290 BIOGER-CPP, INRA, Route de St-Cyr, 78026 Versailles, France

... were improved manually for seven genes, one of which was not predicted by automatic software Blastx alignment data; FGenesh (http://www.softberry.com) and ...


DNA Research
2008 15(2):93-102; doi:10.1093/dnares/dsn001

Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome

Kyujung Van et al.,
Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea

... Also, gene annotation was conducted with the web-based gene prediction programs FGENESH (http://sun1.softberry.com/berry.phtml) and GeneMark (http://exon.gatech ...


Insect Biochemistry and Molecular Biology
Volume 38, Issue 3, March 2008, Pages 331-345

Annotation and expression profiling of apoptosis-related genes in the yellow fever mosquito, Aedes aegypti

Bart Bryanta, Carol D. Blairb, Ken E. Olsonb and Rollie J. Clem
Molecular, Cellular, and Developmental Biology Program, Arthropod Genomics Center, Division of Biology, Ackert Hall, Kansas State University, Manhattan, KS, USA bArthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA

... Genscan (http://genes.mit.edu/GENSCAN.html) and fgenesh (http://www.SoftBerry.com) were used to predict genes and complete missing regions of some EST contigs. ...


Plant Physiology
146:940-951 (2008)

Characterization of the Monoterpene Synthase Gene tps26, the Ortholog of a Gene Induced by Insect Herbivory in Maize

Changfa Lin et al.,
Waksman Institute, Rutgers University, Piscataway, New Jersey 08855 (C.L., B.S., Z.X., H.K.D.); Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901 (B.S., Z.X., H.K.D.);

... Analysis of the sequence by the gene-finding program Fgenesh (www.softberry.com) predicted that, like stc1, tps26 consisted of seven exons. ...


Disease Markers
Volume 24, Number 2 / 2008 Pages 111-117

Analysis of Crohn's disease-related CARD15 polymorphisms in Spanish patients with idiopathic uveitis

N. Rodriguez-Perez, A. Aguinaga-Barrilero, Marina B. Gorrono-Echebarria, Mercedes Perez-Blas, J.M. Marti'n-Villa
Inmunologia, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain Servicio de Oftalmologia, Hospital Universitario Principe de Asturias, Alcala de Henares, Madrid, Spain

... Analysis carried out with GEN- SCAN (http://genes.mit.edu/GENSCAN.html), FCGENESH (http://www.softberry.com/berry.phtml) and GRAIL (http://grail.lsd.ornl.gov ...


Crop Sci
48:S-49-S-68 (2008)

Structural Features of the Endogenous CHS Silencing and Target Loci in the Soybean Genome

Jigyasa H. Tuteja and Lila O. Vodkin
Dep. of Crop Sciences, 384 ERML, 1201 W. Gregory Dr., Univ. of Illinois, Urbana, IL 61801.

... For ab initio predictions, FGeneSH with the Medicago truncatula-based training set (http://www.softberry.com; verified 9 Jan. 2008) was run. ...


Journal of Integrative Plant Biology
Volume 50 Issue 4 Page 466-474, April 2008

Cell-wall Invertases from Rice are Differentially Expressed in Caryopsis during the Grain Filling Stage

Yong-Qin Wang et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100049, China

... Splice site prediction was carried out with programs GENSCAN (http://genes.mit.edu/ GENSCAN.html) and FGENESH (http://www.softberry.com/berry.phtml). ...


Journal of Integrative Plant Biology
Volume 50 Issue 1 Page 62-75, January 2008

Cloning and Expression Analysis of Rice Sucrose Transporter Genes OsSUT2M and OsSUT5Z

Ai-Jun Sun et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China; 2Graduate School of the Chinese Academy of Sciences, Beijing 100049, China

... The ORF of these two potential sucrose transporters were figured out by FGENESH (http://www.softberry.com/), and primers used for RT-PCRs were designed by ...


Molecular Plant
2008 1(3):471-481; doi:10.1093/mp/ssn014

Mutation of a Gene in the Fungus Leptosphaeria maculans Allows Increased Frequency of Penetration of Stomatal Apertures of Arabidopsis thaliana

Candace E. Elliott, Harjono, and Barbara J. Howlett
School of Botany, The University of Melbourne, Melbourne, Vic 3010, Australia Current address: Laboratory of Forest Protection, Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia 55281

... using a primer walking strategy. Genes on the cosmid were predicted using FGENESH software (www.softberry.com). A BLASTp search (www ...


Plant Physiology
146:200-212 (2008)

Recurrent Deletions of Puroindoline Genes at the Grain Hardness Locus in Four Independent Lineages of Polyploid Wheat

Wanlong Li, Li Huang and Bikram S. Gill
Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506–5502

... Protein-coding genes were predicted using the program FGENESH (http://sun1.softberry. com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind) with the ...


Genomics
Volume 91, Issue 5, May 2008, Pages 467-475

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

Nicolas Buisinea 1, Hadi Quesneville, 2 and Vincent Colot
Unite' de Recherche en Ge'nomique Ve'ge'tale, INRA UMR1165–CNRS UMR8114–Universite' d'Evry Val d'Essonne, 2 rue Gaston Cre'mieux, 91057 Evry, France Laboratoire Bioinformatique et Ge'nomique, Institut Jacques Monod, Tour 42, 2 place Jussieu, 75251 Paris, France

... The functional content of each RU sequence was predicted using FGENESH (http://sun1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind ...


Nucleic Acids Research,
2008, Vol. 36, Database issue D298-D302

ChromDB: The Chromatin Database

Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA

... In many cases, we have derived our own transcript models from genomic sequences using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...


Nature Biotechnology
26, 553 - 560 (2008)

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Diego Martinez et al.,
Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico 87545, USA. Novozymes, Inc., 1445 Drew Ave., Davis, California 95618, USA.

... an ab initio gene predictor, Fgenesh 37 , specifically trained for this genome, and two homology-based gene predictors, Fgenesh+ (http://www.softberry.com) and ...


FGENESH 2007

Genome Res.
17:1389-1398, 2007

Conrad: Gene prediction using conditional random fields

David DeCaprio et al.,
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

... data. Conrad was trained on the entire reference set and Fgenesh was trained by Softberry (Salamov and Solovyev 2000 Go). Results. ...


PNAS
July 10, 2007 | vol. 104 | no. 28 | 11844-11849

A GeneTrek analysis of the maize genome

Renyi Liu et al.,
Department of Genetics, University of Georgia, Athens, GA 30602; and Department of Agronomy, Iowa State University, Ames, IA 5001

... BAC sequences were first subject to ab initio gene prediction with FGENESH (www.softberry.com) using the matrix for monocot plants. ...


Antonie van Leeuwenhoek
Volume 91, Number 4 / May, 2007 pp. 373-391

Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides ( Gibberella fujikuroi MP-A)

Anita Keszthelyi et al.,
Agricultural Biotechnology Center, Szent-Gyorgyi A. u. 4, H-2100 Godollo, Hungary

.. Sequence data were analyzed with the Lasergene (DNAStar Inc., Madison, Wisconsin, USA) software package and the FGENESH program (www.softberry.com). ...


Genome
Volume 50, Number 6, 1 June 2007 , pp. 595-609(15)

Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species

Wang, Chih-Li et al.,

... acc. No. DQ312266) using the FGENESH program (http://www.softberry.com) with As- pergillus as the organism parameter (Fig. 1). The ...


Current Genetics
Volume 52, Number 1 / July, 2007 pp. 11-22

Mating-type loci of heterothallic Diaporthe spp.: homologous genes are present in opposite mating-types

Satoko Kanematsu. Yoshihiko Adachi and Tsutae Ito
Apple Research Station, National Institute of Fruit Tree Science, NARO, Shimokuriyagawa, Morioka 020-0123, Japan , National Agricultural Research Center for Tohoku Region, NARO, Akahira, Morioka 020-0198, Japan

... Genes, introns, exons and transcription initiation sites of Diaporthe W- and G-types were predicted by analysis with FGENESH (http://www.softberry.com) on N ...


Plant Molecular Biology
Volume 65, Numbers 1-2 / September, 2007 pp. 189-203

Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome

Shuangcheng Gao et al.,
Key Laboratory of Crop Germplasm & Biotechnology, MOA, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, No. 12 South Street, Zhongguancun, Beijing, 100081, P.R. China

... FGENESH (http://www.softberry.com/ nucleo.html) and GENESCAN (http://genemark. mit.edu/ GENESCAN.htm) were used for gene prediction. ...


Plant Molecular Biology
Volume 65, Number 4 / November, 2007 pp. 439-451

Molecular cloning and expression analysis of a monosaccharide transporter gene OsMST4 from rice ( Oryza sativa L.)

Yongqin Wang et al.,
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing, 100101, China

... Splice site prediction was per- formed with programs GENSCAN (http://www.genes.mit. edu/GENSCAN.html) and FGENESH (http://www. softberry.com/berry.phtml). ...


Plant Physiology
145:29-40 (2007)

Chlorophyll-Deficient Rice Mutant with Impaired Chlorophyllide Esterification in Chlorophyll Biosynthesis

Ziming Wu et al.,
National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China (Z.W., B.H., L.J., C.W., J.W.);

... 2, B and C). Within this region, two open reading frames (ORFs) were predicted using the program FGENESH 2.2 (www.softberry.com). ...


TAG Theoretical and Applied Genetics
Volume 115, Number 2 / July, 2007 pp. 159-168

Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat

Ji-Wen Qiu et al.,
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China

... tauschii lines were translated into protein sequences using the online gene prediction program Fgenesh (http://sunl.Softberry.com/cgi-bin/programs/gWnd/ Fgenesh ...


Fungal Genetics and Biology
Volume 44, Issue 10, October 2007, Pages 1002-1010

Comparison of loline alkaloid gene clusters across fungal endophytes: Predicting the co-regulatory sequence motifs and the evolutionary history

Brandi L. Kutil et al.,
Department of Plant Pathology and Microbiology, Texas A&M University (2132), College Station, TX 77843-2132, USA

.. of coding sequences based on previously identified cDNAs ([Spiering et al., 2002] and [Spiering et al., 2005]) and FGENESH (http://www.softberry.com/berry.phtml ...


Peptides
Volume 28, Issue 6, June 2007, Pages 1282-1291

Neuropeptide precursors in Tribolium castaneum

Andinet Amare and Jonathan V. Sweedler
Department of Chemistry and The Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States

... The FGENESH version 2.5 (www.softberry.com) and Augustus version 1.8.2 (http://augustus.gobics.de/submission) gene prediction programs were used to predict ...


Mol. BioSyst.,
2007, 3, 794 - 802, DOI: 10.1039/b705803a

Distinctive expression and functional regulation of the maize (Zea mays L.) TOR kinase ortholog

Lourdes Teresa Agredano-Moreno, Homero Reyes de la Cruz, Leon Patricio Martinez-Castilla and Estela Sanchez de Jimenez

... OsTOR was obtained with the Gene Builder system (http://www.itba.mi.cnr.it/webgene) and confirmed with the FGENESH 2.4 program from the Softberry webpage (http ...


Plant Physiology and Biochemistry
Volume 45, Issue 1, January 2007, Pages 6-14

Computational identification and phylogenetic analysis of the MAPK gene family in Oryza sativa

Qingpo Liu and Qingzhong Xue
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, No 268, Kaixuan Road, Hangzhou, Zhejiang 310029, China

... Redundant hits were removed by manual inspection. Gene structure prediction was performed using the online web server FGENESH (http://www.softberry.com). 2.2. ...


Fungal Genetics and Biology
Volume 44, Issue 5, May 2007, Pages 415-429

Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum

Ioannis Stergiopoulos et al.,
Laboratory of Phytopathology, Wageningen University and Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands

... Barcelona, Spain) and the FEX (Solovyev et al., 1994) and FGENESH (Salamov and Solovyev, 2000) programs from the MOLQUEST software package (Softberry Inc. ...


Nucleic Acids Research
(2007), doi:10.1093/nar/gkm768

ChromDB: The Chromatin Database

Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA

... In many cases, we have derived our own transcript models from genomic sequences using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...


Microbiology
153 (2007), 3409-3416;

A 7-dimethylallyltryptophan synthase from Aspergillus fumigatus: overproduction, purification and biochemical characterization

Anika Kremer, Lucia Westrich and Shu-Ming Li
Heinrich-Heine-Universitat Dusseldorf, Institut fur Pharmazeutische Biologie und Biotechnologie, Universitatsstrasse 1, D-40225 Dusseldorf, Germany, Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, D-72076 Tubingen, Germany

... FGENESH (Softberry; www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used for intron prediction ...


General and Comparative Endocrinology
Volume 153, Issues 1-3, August-September 2007, Pages 59-63

Evolutionary conservation of bursicon in the animal kingdom

Tom Van Loy et al.,
Animal Physiology and Neurobiology, Laboratory for Developmental Physiology, Genomics and Proteomics, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000, Belgium

... ncbi.nih.gov/gorf) and, in addition, were conducted to the gene prediction program FGENESH based on hidden markov models, available on http://www.softberry.com ...


Fungal Genetics and Biology
Volume 44, Issue 2, February 2007, Pages 77-87

Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium

Phil Kersten and Dan Cullen
Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA

... Predictions were based on ab initio methods Fgenesh (Salamov and Solovyev, 2000), homology-based methods, Fgenesh+ (www.softberry.com) and Genewise (Birney and ...


Molecular Plant Pathology
Volume 8 Issue 1 Page 111-120, January 2007

Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana

LAURA CONDE-FERRAEZ et al.,
Centro de Investigacion Cientifica de Yucatan (CICY), Calle 43 no. 130, Chuburna de Hidalgo, C.P. 97200, Merida, Yucatan, Mexico

... Identification of open reading frames (ORFs) and gene predictions were performed using FGENESH and FGENESH+ software (SoftberryTM, http:/ / www.softberry.com ...


Chinese Science Bulletin
Volume 52, Number 7 / April, 2007 pp. 903-911

Genetic and physical mapping of AvrPi7 , a novel avirulence gene of Magnaporthe oryzae using physical position-ready markers

Feng ShuJie, Wang Ling, Ma JunHong, Lin Fei and Pan QingHua
Laboratory of Plant Resistance and Genetics, College of Natural Resources and Environmental Science, South China Agricultural University, Guangzhou, 510642, China
Laboratory of Plant Protection, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China

... for fine mapping of the Avr gene locus based on the se- quence of the candidate genes predicted using the gene annotation system Softberry FGENESH (http://www. ...


Plant Molecular Biology
Volume 64, Number 5 / July, 2007 589-600

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

Shibo Zhang et al.,
(1) Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA

... BLASTN, BLASTX, and TBLASTX against TIGR’s Rice Gene Indices database and NCBI’s nonredundant and dbEST databases; FGENESH (http:// www.softberry.com/nucleo ...


DNA AND CELL BIOLOGY
Volume 26, Number 6, 2007 Pp. 369-385

Genomics, Evolution, and Expression of TBPL2, a Member of the TBP Family

CINZIA DI PIETRO et al.,
Dipartimento di Scienze Biomediche-Unita` di Biologia Genetica e BioInformatica, Universita` di Catania, Catania, Italy, EU.

Genomic sequences were analyzed using several gene prediction tools (GPTs): Genescan (http://genes.mit.edu/GENSCAN.html), GeneMark (http://opal.biology.gatech.edu/GeneMark/index .html), FGENESH (http://www.softberry.com/berry.phtml?topic =gfind&prg=FGENESH),


Chinese Science Bulletin
Volume 52, Number 7 / April, 2007 912-921

Rapid genome evolution in Pms1 region of rice revealed by comparative sequence analysis

Yu JinSheng et al.,
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China

... For gene prediction, the sequences were ana- lyzed with several gene prediction programs including FGENESH (monocot training set, http://www.softberry. ...


Journal of Integrative Plant Biology
Volume 49 Issue 5 Page 655-663, May 2007

The 6-phosphogluconate Dehydrogenase Genes Are Responsive to Abiotic Stresses in Rice

Fu-Yun Hou, Ji Huang, Shan-Lin Yu and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China

... One assembled cDNA sequence containing a complete ORF (opening reading frame) of 1 524 bp was obtained using the FGENESH program (http://www.softberry.com) and ...


Molecular Plant Pathology
Volume 8 Issue 3 Page 307-319, May 2007

Molecular and cytological responses of Medicago truncatula to Erysiphe pisi

DAWN FOSTER-HARTNETT et al.,
Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, St Paul, MN 55108, USA

... BAC sequences with > 98% identity were collected, corresponding coding regions were predicted using FGENESH software (http://www.softberry.com), and the 1.5-kb ...


Plant Science
Volume 172, Issue 4, April 2007, Pages 708-721

Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.)

R. Naga Amruthaa, P. Nataraj Sekhara, Rajeev K. Varshneyb and P.B. Kavi Kishora,
aDepartment of Genetics, Osmania University, Hyderabad 500007, India
bInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502325, India

... and Karlin, 1997; http:// genes.mit.edu/GENSCAN.html), GenomeScan [30]; http://genes.mit.edu/ genomescan.html), FGENESH [31]; http://www.softberry.com/berry ...


Molecular Biology and Evolution, 2007, doi:10.1093/molbev/msm116

PIF-like Transposons Are Common in Drosophila and Have Been Repeatedly Domesticated to Generate New Host Genes

Claudio Casola, A. Michelle Lawing, Esther Betran and Cedric Feschotte
Department of Biology University of Texas, Arlington

... The structure of each DPLG coding sequence was initially predicted using FGENESH (http://www.softberry.com/berry.phtml) and refined by multialignment with ...


Journal of Virology,
June 2007, p. 6491-6501, Vol. 81, No. 12

Genomic and Morphological Features of a Banchine Polydnavirus: Comparison with Bracoviruses and Ichnoviruses

Renee Lapointe et al.,
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, Quebec, Quebec G1V 4C7, Canada

... html), the Gene Construction Kit 2 program (Texco Inc.), Genchek v. 2061 (Ocimum Biosolutions), and FGENESH, with the Apis mellifera settings (www.softberry.com ...


The Plant Journal
Volume 49 Issue 2 Page 173-183, January 2007

Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species

Ki-Byung Lim et al.,
1School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea,
2Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea,

... Gene annotation was achieved using the web-based gene prediction program FGENE-SH Arabidopsis ( http:/ / www.softberry.com/ berry.phtml ). Sequence analysis. ...


Journal of Molecular Evolution
Volume 64, Number 3 / March, 2007 354-363

Molecular Phylogeny, Evolution, and Functional Divergence of the LSD1-Like Gene Family: Inference from the Rice Genome

Qingpo Liu 1 and Qingzhong Xue 1
(1) Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, P. R. China

... The FGENESH software (http://www.softberry.com) was used to predict the intron/exon structure of putative rice LSD1-like genes. ...


BMC Microbiology
2007, 7:61 doi:10.1186/1471-2180-7-61

Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus

Christopher A Desjardins et al.,
The Institute for Genomic Research, a division of J. Craig Venter Institute, Rockville, Maryland, USA

...A combination of Softberry's FGENESH trained on the honey bee (Apis mellifera) and the Beijing Genome Institute's BGF trained on the silkmoth (Bombyx mori) were most accurate ...
...Gene models were generated with a variety of software: Softberry's FGENESH [77] using both the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster) training sets,...


PNAS
| May 1, 2007 | vol. 104 | no. 18 | 7705-7710

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Brian Palenik et al.,
aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304;

... Gene prediction methods used for annotation of two Ostreococcus genomes included ab initio Fgenesh (40), homology-based Fgenesh+ (SoftBerry), Genewise (41 ...


Nature Biotechnology
25, 319 - 326 (2007) Published online: 4 March 2007 | doi:10.1038/nbt1290

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Thomas W Jeffries et al.,
US Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin 53705, USA.
Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, Wisconsin 53706, USA.

... Gene prediction methods used for analysis of the P. stipitis genome include ab initio Fgenesh 44 , homology-based Fgenesh+ (http://www.softberry.com/) and ...


Functional & Integrative Genomics
Volume 7, Number 1 / January, 2007 17-35

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes

Nagendra K. Singh et al.,
Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

... Gene prediction was performed on individual BAC/PAC clones using FGENESH trained for monocot species (http://www.softberry.com) (Salamov and Solovyev 2000). ...


Molecular Microbiology
Volume 64 Issue 3 Page 755-770, May 2007

Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae

Huiqin Chen, Miin-Huey Lee, Margret E. Daub, Kuang-Ren Chung
Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA.

... positions were deduced from comparisons of genomic and cDNA sequences and/or predicted using the fgenesh gene-finding software at http://www.softberry.com. ...


Plant Physiology
144:623-636 (2007)

Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants

Xue-Cheng Zhang et al.,
Division of Plant Sciences and National Center for Soybean Biotechnology (X.-C.Z., X.W., S.F., J.W., M.L., H.T.N., G.S.) and Division of Biochemistry, Department of Molecular Microbiology and Immunology (G.S.), University of Missouri, Columbia, Missouri 65211; and United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.B.C.)

... Center. BAC sequences were annotated using the dicot species model and Arabidopsis matrix of FGENESH (www.softberry.com). Annotated ...


FGENESH 2006

Nature
443, 931 - 949 (26 Oct 2006)

Insights into social insects from the genome of the honeybee Apis mellifera

The Honeybee Genome Sequencing Consortium

...to produce a master gene list: the Official Gene Set (OGS). The component gene sets were from NCBI, Ensembl, Softberry (Fgenesh), an evolutionarily conserved core set and a set based on Drosophila orthologues (Supplementary...


PNAS
| October 24, 2006 | vol. 103 | no. 43 | 15794-15799

Vitamin K-dependent proteins in Ciona intestinalis, a basal chordate lacking a blood coagulation cascade

John D. Kulman*, Jeff E. Harris*, Noriko Nakazawa, Michio Ogasawara, Masanobu Satake, and Earl W. Davie*,
*Department of Biochemistry, University of Washington, Seattle, WA 98195; Department of Biology, Faculty of Science, Chiba University, Chiba 263-8522, Japan; and Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan

... scaffolds. The resulting sequences were analyzed for probable intron/exon boundaries with FGENESH (Softberry, Mount Kisco, NY). ...


TAG Theoretical and Applied Genetics
Volume 113, Number 6 / October, 2006 1147-1158

The barley serine/threonine kinase gene Rpg1 providing resistance to stem rust belongs to a gene family with five other members encoding kinase domains

R. Brueggeman 1 , T. Drader 2 and A. Kleinhofs 1, 2
(1) Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA
(2) School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4234, USA

... gene struc- tures were predicted by sequence comparison with the Rpg1 cDNA sequence and using the FGENESH gene prediction program (http://www.softberry.com). ...


Annual Review of Phytopathology
Vol. 44: 337-366 (Volume publication date September 2006)

The Dawn of Fungal Pathogen Genomics

Jin-Rong Xu,1 ­ You-Liang Peng,2 ­ Martin B. Dickman,3 and ­ Amir Sharon4­
1Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907

... at the Broad Institute, gene structures are predicted using the Calhoun annotation system that is a combination of FGENESH (http://www.softberry.com), FGENESH+ ...


Insect Molecular Biology
Volume 15 Issue 5 Page 597-602, October 2006

Expression of insulin pathway genes during the period of caste determination in the honey bee, Apis mellifera

D. E. Wheeler, N. Buck, J. D. Evans
Department of Entomology, University of Arizona, Tucson AZ USA, USDA ARS, Bee Research Laboratory, Beltsville, MD 20705 USA

... Primers were designed based on cDNA sequences from the official gene list or on the basis of FGENESH ( http:/ / www.softberry.com ) predictions of genomic ...


BMC Genomics.
2006; 7: 321

Quantitative analysis of cell-type specific gene expression in the green alga Volvox carteri

Ghazaleh Nematollahi,#1 Arash Kianianmomeni,#1 and Armin Hallmann1
1Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitatsstr. 25, D-33615 Bielefeld, Germany

...Exon-intron prediction of Volvox genes was done using FGENESH software (Softberry, Mount Kisco, NY) and by polypeptide sequence comparisons with homologs from other organisms using ...


Developmental Biology
300 (2006) 2-8

Shedding genomic light on Aristotle's lantern

Erica Sodergren et al.,
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA

...using software developed at Ensembl (Potter et al., 2004; Sea Urchin Genome Sequencing Consortium, 2006) and installed at BCM-HGSC, NCBI (gnomon software; Souvorov et al., 2004), Softberry (FgenesH software; Salamov and Solovyev, 2000; Solovyev, 2001),...


Genetics.
2006 November; 174(3): 1493 - 1504.

Types and Rates of Sequence Evolution at the High-Molecular-Weight Glutenin Locus in Hexaploid Wheat and Its Ancestral Genomes

Yong Qiang Gu et al.,
United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710

...FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark.mit.edu/GENESCAN.htm) were used for gene prediction...


DNA Sequence,
Volume 17, Issue 3 June 2006 , pages 223 - 230

Isolation and characterization of the RanGAP gene in the mosquito Aedes aegypti

Sung-Jae Cha a; Neil Lobo b; Becky Debruyn b; David W. Severson b
a Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Malaria Research Institute. Baltimore, MD. USA
b Department of Biological Sciences, Center for Tropical Disease Research and Training, University of Notre Dame. Notre Dame, IN. USA

... submitted to two gene finding programs: GENSCAN (http://genes.mit.edu/ GENSCAN.html) using the vertebrate database and FGENESH (http://www.softberry.com/berry ...


Molecular Plant Pathology
Volume 7 Issue 6 Page 485-497, November 2006

The global nitrogen regulator, FNR1, regulates fungal nutrition-genes and fitness during Fusarium oxysporum pathogenesis

HEGE HVATTUM DIVON, CARMIT ZIV, OLGA DAVYDOV, ODED YARDEN, ROBERT FLUHR
1Department of Plant Science, Weizmann Institute of Science, 76100 Rehovot, Israel

... The sequence was, in the Softberry gene prediction database ( http:/ / www.softberry.com/ berry.phtml ; FGENESH), predicted to contain an open reading ...


Genetics.
2006 October; 174(2): 1017-1028.

Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)

Jessica A. Schlueter,* Brian E. Scheffler, Shannon D. Schlueter,* and Randy C. Shoemaker‡1
*Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USDA-ARS MSA Genomics Laboratory, Stoneville, Mississippi 38776 and ‡USDA-ARS-CICGR, Ames, Iowa 50011

... Genscan with Arabidopsis thaliana-based parameters (Burge and Karlin 1997), FgeneSH with Medicago truncatula-based parameters (http://www.softberry.com) and ...


Applied and Environmental Microbiology,
October 2006, p. 6527-6532, Vol. 72, No. 10

The Homologue of het-c of Neurospora crassa Lacks Vegetative Compatibility Function in Fusarium proliferatum

Zoltan Kerenyi,1 Brigitta Olah,1,2 Apor Jeney,1 Laszlo Hornok,1,2 and John F. Leslie3*
Agricultural Biotechnology Center, Szent-Gyorgyi A. u. 4., H-2100 Godoll, Hungary,
1 Department of Agricultural Biotechnology and Microbiology, Mycology Group, Hungarian Academy of Sciences, Szent Istvan University, Pater K. u. 1., H-2103 Godoll, Hungary,
2 Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506-55023

... Sequence data were analyzed with the Lasergene software package (DNAStar Inc., Madison, Wis.) and the FGENESH program (http://www.softberry.com). ...


Genetics
2006 November; 174(3): 1671 - 1683

Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize

Yan Fu et al.,
*Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa 50011, Department of Agronomy, Iowa State University, Ames, Iowa 50011

... 2004) alignments between genomic and EST sequences or predicted using FGENESH (http://www.softberry.com) as described (Yao et al. 2005). ...


ChemBioChem
2006 Volume 7, Issue 1 , Pages 158 - 164

Reverse Prenyltransferase in the Biosynthesis of Fumigaclavine C in Aspergillus fumigatus: Gene Expression, Purification, and Characterization of Fumigaclavine C Synthase FGAPT1

Inge A. Unsold, Shu-Ming Li, Priv. Doz. Dr. *
Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tubingen, Germany,

... FGENESH (Softberry, Inc., www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1: Hitachi Software Engineer- ing, San Bruno, CA) were used ...


Fungal Genetics and Biology
43 (2006) 316-325

Development of a Fusarium graminearum AVymetrix GeneChip for proWling fungal gene expression in vitro and in planta

Ulrich Guldener et al.,
Technische Universität Munchen, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany

... to the automatically pre- dicted set from the Broad Institute, a second automatic gene call set was developed at MIPS using FGENESH (www.softberry.com) with a ...


The Journal of Clinical Endocrinology & Metabolism
2006 Vol. 91, No. 11 4587-4592

Identification of Three Novel Mutations in the GATA3 Gene Responsible for Familial Hypoparathyroidism and Deafness in the Chinese Population

Wei-Yih Chiu, Huan-Wen Chen, Hwei-Wen Chao, Lee-Tzong Yann and Keh-Sung Tsai
Departments of Laboratory Medicine (W.-Y.C., H.-W.Cha, K.-S.T.) and Internal Medicine (W.-Y.C., L.-T.Y, K.-S.T.), National Taiwan University Hospital, Taipei 100, Taiwan; and Department of Internal Medicine (H.-W.Che), Lo-Tung Pohai Hospital, Ilan 256, Taiwan

... is useful. We used the FGENESH program (www.softberry.com) based on the consensus sequence of exon-intron junctions (ag ... gt rule ...


CURRENT SCIENCE
VOL. 91, NO. 4, 25 AUGUST 2006 510-515

Bioinformatics approach toward identification of candidate genes for zinc and iron transporters in maize

R. S. Chauhan
Bioinformatics Centre, Advanced Centre of Hill Bioresources and Biotechnology, CSK HP Agricultural University, Palampur 176 062, India

... using gene prediction algorithms of FGenesH 18 (http://www.softberry.com/ berry.phtml? topic= fgenesh&group=programs&subgroup=gfind ...


Acta Biochimica et Biophysica Sinica
Volume 38, Number 11, November 2006 , pp. 812-820(9)

Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

SUN, Xiao-Ming et al.,
Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China

... Gene prediction was carried out using GENSCAN (http://genes.mit.edu/GENSCAN. html) and FGENESH (http://www.softberry.com/berry.html). ...


Functional & Integrative Genomics
Volume 6, Number 4 / October, 2006 pp. 338-341

Drought tolerance genes in rice

Huazong Zeng, Yang Zhong and Lijun Luo
Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, 200433, People’s Republic of China
Shanghai Agro-Biological Gene Center, Shanghai, 201106, People’s Republic of China

... ncbi.nih.gov/) through BLAST. After this, Fgenesh soft- ware (http://www. softberry.com) was used to predict candidate genes. All ...


Genome
Volume 49, Number 3, 1 March 2006, pp. 209-218(10)

Molecular structure and organization of the wheat genomic manganese superoxide dismutase gene

Baek, Kwang-Hyun; Skinner, Daniel Z.; Ling, Peng; Chen, Xianming

... softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind; Salamov and Solovyev 2000) and GeneScan (http://genes.mit.edu/GENSCAN. ...


Nucleic Acids Research
2006 34(17):4685-4701

Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae

Cathryn Rehmeyer et al.,
Department of Plant Pathology, University of Kentucky Lexington, KY 40546 USA

... The masked sequences were then used for gene prediction with Fgenesh (67) trained on M.oryzae sequences (Softberry, www.softberry.com). ...


TAG Theoretical and Applied Genetics
Volume 113, Number 5 / September, 2006 pp.875-883

Identification and fine mapping of AvrPi15, a novel avirulence gene of Magnaporthe grisea

Jun-Hong Ma et al.,
Laboratory of Plant Resistance and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou, 510642, China

... out with the CAG markers, which were developed based on the sequence of the candidate genes predicted using the gene annotation system, Softberry FGENESH ...


The Plant Cell
18:1339-1347 (2006)

Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa

Yang et al.,
Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea

... Gene annotation was achieved using the web-based gene prediction program FGENESH Arabidopsis (http://www.softberry.com/berry.phtml). ...


Genome Research
16:618-626, 2006

Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice

He et al.,
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China

... 1997 Go) programs. Sequence analysis and gene prediction were performed by using the gene-finding programs FGENESH (http://www.softberry.com/berry.phtml). ...


Molecular Genetics and Genomics
Volume 275, Number 5 / May, 2006 pp. 450-459

Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)

Dariusz Grzebelus, Yuan-Yeu Yau and Philipp W. Simon
Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425 Krakow, Poland
USDA-ARS Vegetable Crops Research Unit and Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA

... ORF and exon/intron localization were predicted using GenScan (URL: http://www.genes. mi- t.edu/GENSCAN.html) and FGenesh (URL: http:// www.softberry.com). ...


Planta
Volume 223, Number 6 / May, 2006 pp. 1134-1144

Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog

Venkatesh et al.
Monsanto Company, 800 N. Lindbergh Boulevard, St. Louis, MO 63167, USA

... http://hmmer.wustl.edu/). Gene prediction software FGENESH was procured from Softberry Inc., NY, USA. Dicot model provided with ...


Development Genes and Evolution
Volume 216, Number 4 / April, 2006 pp. 198-208

A comparative study of sperm morphology, cytology and activation in Caenorhabditis elegans, Caenorhabditis remanei and Caenorhabditis briggsae

Geldziler et al.
Department of Genetics, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA

... The genome sequence around the sequence thus identified was used as an input for the gene prediction algorithms FGeneSH (http://www.softberry.com/berry. ...


Mol. Ecol.
Volume 15 Issue 5 Page 1367 -1378. April 2006

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa

Gilchrist et al.
Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4

... Gene models were predicted using fgenesh (Salamov & Solovyev 2000) through the Softberry website ( http:/ / www.softberry.com ). ...


Genome Research
16:618-626, 2006

Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice

Guangming He et al.
1 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China;

... 1997 Go) programs. Sequence analysis and gene prediction were performed by using the gene-finding programs FGENESH (http://www.softberry.com/berry.phtml). ...


The Plant Cell
18:1339-1347 (2006)

Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa[W],[OA]

Tae-Jin Yanga et al.
a Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea

... Gene annotation was achieved using the web-based gene prediction program FGENESH Arabidopsis (http://www.softberry.com/berry.phtml). ...


Medical Mycology
Publisher: Taylor & Francis Issue: Volume 44, Number 3 / May 2006 Pages: 211 - 218

The role of the sakA (Hog1) and tcsB (sln1) genes in the oxidant adaptation of Aspergillus fumigatus

Chen Du A1, Jacqueline Sarfati A2, J-P Latge A2, Richard Calderone A1
A1 Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, USA A2 Aspergillus Unit, Institut Pasteur, Paris, France

... tcsB gene and phenotype of the deletion mutant DNA sequence analysis of tcsB (gene-finding software FGENESH. WWW.softberry.com) revealed a long Fig. ...


Molecular Genetics and Genomics
Issue: Volume 275, Number 5 Date: May 2006 Pages: 504 - 511

A complete physical map of a wild beet (Beta procumbens) translocation in sugar beet

Daniela Schulte1, Daguang Cai1, Michael Kleine1, 2, Longjiang Fan1, 3, Sheng Wang1, 3 and Christian Jung1
(1) Plant Breeding Institute, Christian-Albrechts-University Kiel, Olshausenstr. 40, 24098 Kiel, Germany (2) Present address: PLANTON GmbH, Am Kiel-Kanal 44, 24106 Kiel, Germany (3) Institute of Bioinformatics and Institute of Crop Science, Zhejiang University, 310029 Hangzhou, China

... An ab initio ORF-analysis with the FgeneSH program on http://www.sun1.softberry. com was performed to iden- tify putative coding regions using the A. thaliana ...


Molecular Genetics and Genomics
Issue: Volume 275, Number 5 Date: May 2006 Pages: 450 - 459

Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)

Dariusz Grzebelus1, Yuan-Yeu Yau2, 3, 4 and Philipp W. Simon2
(1) Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425 Krakow, Poland

... ORF and exon/intron localization were predicted using GenScan (URL: http://www.genes. mi- t.edu/GENSCAN.html) and FGenesh (URL: http:// www.softberry.com). ...


Development Genes and Evolution
Issue: Volume 216, Number 4 Date: April 2006 Pages: 198 - 208

A comparative study of sperm morphology, cytology and activation in Caenorhabditis elegans, Caenorhabditis remanei and Caenorhabditis briggsae

Brian Geldziler1, Indrani Chatterjee1, Pavan Kadandale1, Emily Putiri1, Rajesh Patel2 and Andrew Singson1
(1) Department of Genetics, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA (2) Department of Pathology, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA

... The genome sequence around the sequence thus identified was used as an input for the gene prediction algorithms FGeneSH (http://www.softberry.com/berry. ...


Planta
Issue: Volume 223, Number 6 Date: May 2006 Pages: 1134 - 1144

Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog

Tyamagondlu V. Venkatesh1, Balasulojini Karunanandaa1, Daniel L. Free2, Jeannie M. Rottnek2, Susan R. Baszis2 and Henry E. Valentin3
(1) Monsanto Company, 800 N. Lindbergh Boulevard, St. Louis, MO 63167, USA

... http://hmmer.wustl.edu/). Gene prediction software FGENESH was procured from Softberry Inc., NY, USA. Dicot model provided with ...


TAG Theoretical and Applied Genetics
Issue: Volume 112, Number 6 Date: April 2006 Pages: 1179 - 1191

Molecular cytogenetics and DNA sequence analysis of an apomixis-linked BAC in Paspalum simplex reveal a non pericentromere location and partial microcolinearity with rice

Ornella Calderini1, Song B. Chang2, 6, Hans de Jong2, Alessandra Busti1, Francesco Paolocci1, Sergio Arcioni1, Sacco C. de Vries3, Marleen H. C. Abma-Henkens4, Rene M. Klein Lankhorst4, Iain S. Donnison5 and Fulvio Pupilli1
(1) Institute of Plant Genetics CNR, Perugia via della madonna alta 130, 06128 Perugia, Italy

... Gene structure and predicted protein sequences were obtained from assembled contigs using the FGENESH program at the SoftBerry site (http://www.softberry.com ...


ChemBioChem
2006, Volume 7, Issue 1 , Pages 158 - 164

Reverse Prenyltransferase in the Biosynthesis of Fumigaclavine C in Aspergillus fumigatus: Gene Expression, Purification, and Characterization of Fumigaclavine C Synthase FGAPT1

Inge A. Unsold, Shu-Ming Li, Priv. Doz. Dr.
Eberhard-Karls-Universitat Tubingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tubingen, Germany, Fax: (+49) 7071-29-5250;

... FGENESH (Softberry, Inc., www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1: Hitachi Software Engineer- ing, San Bruno, CA) were used ...


Genetics
Genetics, Vol. 173, 131-149, May 2006

Searching for neuronal left/right asymmetry: Genome wide analysis of nematode receptor-type guanylyl cyclases

Christopher O. Ortiz et.al.,
Howard Hughes Medical Institute Department of Biochemistry and Molecular Biophysics Columbia University Medical Center 701 W.168th Street New York, NY 10032

... Wormbase WS149), we suspected that C. briggsae genes may have been incorrectly predicted. We therefore ran the FGENESH program at www.softberry.com (S ALAMOV ...


Genome Biology
2006, 7:R16 doi:10.1186/gb-2006-7-2-r16

The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae

Michael R Thon et al.,
Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA

The gene prediction program FGENESH (Softberry Corporation, Mount Kisco, NY, USA) trained to predict M. oryzae genes [3] was used to identify 1,151 putative gene coding sequences.


Genetics
Published Articles Ahead of Print, published on February 19, 2006 as 10.1534/genetics.105.054791

Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps.

Jeong-Hwan Mun et al.,
Department of Plant Pathology, University of California, Davis, CA, USA.

... Gene-coding regions were predicted in M. truncatula using the eudicot version of FGENESH (www.softberry.com). BAC-end sequences were divided into gene- ...


Theor Appl Genet
(2006) DOI 10.1007/s00122-005-0201-2

Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris

James Kami, Vale´ rie Poncet, Vale´ rie Geffroy, Paul Gepts
Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Mailstop 1, 1 Shields Avenue, Davis, CA 95616-8780, USA

... www.genes.cs.wustl.edu/), and FGENESH (http:// www.softberry.com/; trained with Nicotiana tabacum, Medicago truncatula, Dicot or Monocot). ...


Molecular Ecology
15 (5), 1367-1378. - April 2006

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa

ERIN J. GILCHRIST et al.,
Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4

... Gene models were predicted using fgenesh (Salamov & Solovyev 2000) through the Softberry website ( http:/ / www.softberry.com ). ...


Applied and Environmental Microbiology
, March 2006, p. 1793-1799, Vol. 72, No. 3

Characterization of Two Polyketide Synthase Genes Involved in Zearalenone Biosynthesis in Gibberella zeae

Iffa Gaffoor1 and Frances Trail1,2
Departments of Plant Biology,1 Plant Pathology, Michigan State University, East Lansing, Michigan 488242

... portions of the sequence. Using this complete sequence, FGENESH software (http://www. softberry. com) with organism-specific parameters ...


Medical Mycology
Volume 44, Number 3 / May 2006 Pages: 211 - 218

The role of the sakA (Hog1) and tcsB (sln1) genes in the oxidant adaptation of Aspergillus fumigatus

Chen Du A1, Jacqueline Sarfati A2, J-P Latge A2, Richard Calderone A1
A1 Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC, USA A2 Aspergillus Unit, Institut Pasteur, Paris, France

... tcsB gene and phenotype of the deletion mutant DNA sequence analysis of tcsB (gene-finding software FGENESH. WWW.softberry.com) revealed a long Fig. ...


Genetics
Vol. 172, 2491-2499, April 2006

Tracing Nonlegume Orthologs of Legume Genes Required for Nodulation and Arbuscular Mycorrhizal Symbioses

Hongyan Zhu1, Brendan K. Riely2, Nicole J. Burns3, Jean-Michel Ané3
1Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546

... GenBank database. Gene prediction was performed by FGENESH (http://www. softberry.com/berry.phtml?topic=gfind). Sequence alignments ...


TAG Theoretical and Applied Genetics
Issue: Volume 112, Number 4 Date: February 2006 Pages: 618 - 626

Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii

Steven A. Brooks1, 3, Li Huang2, Marie N. Herbel2, Bikram S. Gill2, Gina Brown-Guedira1 and John P. Fellers1
(1)Plant Science and Entomology Unit, Department of Plant Pathology, USDA-ARS, Manhattan, KS 66506, USA

... FGENESH 1.1 (http:// www.softberry.com) was used for coding sequence (CDS) prediction with monocot genomic DNA param- eters. Putative ...


Plant Physiology
, March 2006, Vol. 140, pp. 998-1008

Point Mutations with Positive Selection Were a Major Force during the Evolution of a Receptor-Kinase Resistance Gene Family of Rice

Xinli Sun, Yinglong Cao and Shiping Wang
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

... 1997 Go). The gene prediction programs used were GENSCAN (Burge and Karlin, 1997 Go) and FGENESH (http://www.softberry.com). The ...


Mol Gen Genomics
Volume 275, Number 5 / May, 2006 pp. 504-511

A complete physical map of a wild beet ( Beta procumbens) translocation in sugar beet

Daniela Schulte, Daguang Cai, Michael Kleine, Longjiang Fan, Sheng Wang, Christian Jung
Plant Breeding Institute, Christian-Albrechts-University Kiel, Olshausenstr. 40, 24098 Kiel, Germany

... An ab initio ORF-analysis with the FgeneSH program on http://www.sun1.softberry. com was performed to iden- tify putative coding regions using the A. thaliana ...


Molecular Microbiology
2006, 60 (1), 67-80

Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans

Lilian Gout 1 et al.,
Phytopathologie et Methodologies de la Detection, INRA, F-78026 Versailles, France.

... genscan ( http:/ / genes.mit.edu/ GENSCAN.html ) was used with vertebrate and Arabidopsis settings and fgenesh ( http:/ / www.softberry.com ) was set with N ...


J Gen Virol
87 (2006), 311-322

Characterization and transcriptional analysis of protein tyrosine phosphatase genes and an ankyrin repeat gene of the parasitoid Glyptapanteles indiensis polydnavirus in the parasitized host

D. E. Gundersen-Rindal and M. J. Pedroni
US Department of Agriculture, Agricultural Research Service, Insect Biocontrol Laboratory, Bldg 011A, Room 214, BARC West, Beltsville, MD 20705, USA

... nih.gov/gorf/gorf.html (only large ORFs are shown)], FGENESH [ab initio ... gambiae and Apis mellifera insect gene parameters; http://www.softberry.com (Salamov & ...


FGENESH 2005

Current Biology
2005, Volume 15, Issue 16, Pages 1508-15

Select a website below to get this article

Causier et al.,

... 25], GeneMark.hmm (http://opal.biology.gatech.edu/genemark/eukhmm.cgi) [26] (each with the Arabidopsis dataset), and FGENESH (http://www.softberry.com/) (with ...


Plant Molecular Biology
Volume 58, Number 6 / August, 2005, pp. 809-822

The Medicago truncatula SUNN Gene Encodes a CLV1-like Leucine-rich Repeat Receptor Kinase that Regulates Nodule Number and Root Length

Elise et al.,
(1) Department of Genetics, Biochemistry and Life Science Studies, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA (2) Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche, CNRS-INRA, 31326 Castanet-Tolosan cédex, France

... Genes in this region were predicted using FGENESH (http:// www.softberry.com) (Salamov and Solovyev, 2000) using parameters for the M. truncatula genome, the ...


TAG Theoretical and Applied Genetics
Volume 111, Number 3 / August, 2005, pp. 467-478

Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions

Yang et al.,
(1) Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon, 441-707, Korea (2) Arizona Genomics Institute, University of Arizona, 303 Forbes building, Tucson, AZ 85721, USA

... while the detection of putative genes was analyzed using sev- eral web-based gene prediction programs including: FGENE-SH MONOCOT (http://www.softberry.com/ber ...


Chromosoma
Volume 114, Number 2 / July, 2005, pp. 103-117

In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons

Yang et al.,
(1) Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), RDA, Suwon, 441-707, South Korea (2) Arizona Genomics Institute, 303 Forbes building, University of Arizona, Tucson, AZ 85721, USA

... Gene an- notation was achieved using several web-based gene pre- diction programs such as FGENE-SH Arabidopsis (http:// www.softberry.com/berry.phtml ...


Journal of Molecular Evolution
Volume 61, Number 4 / October, 2005, pp. 559-569

Plant Photoreceptors: Phylogenetic Overview

Patricia Lariguet1 and Christophe Dunand1
(1) Department of Plant Biology, University of Geneva, Quai Ernest Ansermet 30, Geneva 4, CH-1211, Switzerland

... quences were analyzed for the presence of the gene with different programs such as FGenesh (http://www.softberry.com/ber- ry.phtml) and GenScan (http://genes ...


Journal of Molecular Evolution
Volume 60, Number 5 / May, 2005, pp. 615-634

Structure, Evolution, and Expression of the Two Invertase Gene Families of Rice

Xuemei Ji1, 2, Wim Van den Ende3, Andre Van Laere3, Shihua Cheng2 and John Bennett 1
1) Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, DAPO, 7777, Metro Manila, Philippines (2) Chinese National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, Zhejiang, 310006, China

... supplemented the above methods with the use of Genscan (http://genes.mit.edu/ GENSCAN.html) (Burge and Karlin 1997) and FGENESH (http://www.softberry.ru/berry ...


Genetics
Published Articles Ahead of Print: May 6, 2005, Copyright © 2005 doi:10.1534/genetics.105.041616

Centric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile

Lin et al.,
1 Purdue University 2 USDA-ARS-CICGR, and Department of Agronomy 3 University of Minnesota

... Fifteen potential genes were found on the BAC using FGENESH (http://www.softberry. com/berry.phtml) (Table 2). Three of the fifteen (4-6) ...


TAG Theoretical and Applied Genetics
Volume 111, Number 6 / October, 2005, pp. 1080-1086

Delimitation of the rice wide compatibility gene S5n to a 40-kb DNA fragment

Qiu et al.,
(1) National Key Laboratory of Crop Genetic Improvement, and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan, 430070, China

... Gene prediction analysis of the 40-kb DNA fragment using FGENSH (http://www.softberry. com) identified five putative open reading frames (ORFs; Fig. 2). Both ...


Molecular Genetics and Genomics
Volume 274, Number 6 / December, 2005, pp. 569-578

High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea

Sharma et al.,
(1) National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

... The 143,537 bp region of Nipponbare identified by physical mapping was then analysed with FGENESH software (http://www.softberry.com) to detect putative genes. ...


Genetics
2005 July; 170(3): 1221–1230. doi: 10.1534/genetics.105.041616.

Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile

Lin et al.,
*Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 †Purdue University Genomics Core, Department of Horticulture, Purdue University, West Lafayette, Indiana 47907

... Fifteen potential genes were found on the BAC using FGENESH (http://www.softberry. com/berry.phtml) (Table 2). Three of the 15 (4-6) were derived from either ...


Genomics
Volume 85, Issue 6, June 2005, Pages 666-678

Biosilica formation in spicules of the sponge Suberites domuncula: Synchronous expression of a gene cluster

Schroder et al.,
aInstitut fur Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Johannes Gutenberg-Universitat, Duesbergweg 6, D-55099 Mainz, Germany

... Four open reading frames (ORFs) were predicted using the program FGENESH ("softberry"): putative ankyrin repeat protein ANKrp_SUBDO (SDANKrp), silicatein ...


Genetics
2005 February; 169(2): 891–906. doi: 10.1534/genetics.104.034629.

Structure and Evolution of the r/b Chromosomal Regions in Rice, Maize and Sorghum

Zuzana Swigonova,* Jeffrey L. Bennetzen,†1 and Joachim Messi
*Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020 †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392

... Finnzyme, Helsinki). Sequence analysis: Genes predicted by FGENESH (http://www.softberry.com/berry.phtml? topic=gfind&prg=FGENESH ...


Genetics
2005 March; 169(3): 1403–1414. doi: 10.1534/genetics.104.035972.

Gene Clusters for Insecticidal Loline Alkaloids in the Grass-Endophytic Fungus Neotyphodium uncinatum

Martin J. Spiering,* Christina D. Moon,*1 Heather H. Wilkinson,† and Christopher L. Schardl*2
*Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0312 †Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132

... with the search parameters for the N. crassa genome, genomic DNA sequences were entered into the FGENESH gene prediction program (http://www.softberry.com/berry ...


Genetics
2005 July; 170(3): 1209–1220. doi: 10.1534/genetics.105.040915.

DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes

Jianxin Ma,*† Phillip SanMiguel,‡ Jinsheng Lai,§ Joachim Messing,§ and Jeffrey L. Bennetzen*†1
Department of Genetics, University of Georgia, Athens, Georgia 30602 †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907

... Sequence analysis and annotation: Gene-finding programs FGENESH (http://www.softberry. com/berry.phtml?topic=gfind&prg=FGENESH) with the monocot training set ...


PNAS
August 23, 2005 vol. 102 no. 34 12282-12287

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes

Yan Fu et al.,
*Interdepartmental Genetics Graduate Program, §Interdepartmental Bioinformatics and Computational Biology Graduate Program, **L. H. Baker Center for Bioinformatics and Biological Statistics

... fgenesh (Softberry, Mount Kisco, NY) was used for ab initio gene prediction with monocot parameters and the GC option that uses all potential GC donor splice ...


PNAS
December 27, 2005 vol. 102 no. 52 19243-19248

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

Devos et al.,
Departments of *Crop and Soil Sciences, †Plant Biology, and §Genetics, University of Georgia, Athens, GA 30602

... The gene prediction program fgenesh, with the monocot (maize, rice, wheat, and barley) training set (www.softberry.com), was used to predict genes. ...


Eukaryotic Cell
November 2005, p. 1926-1933, Vol. 4, No. 11

Functional Analysis of the Polyketide Synthase Genes in the Filamentous Fungus Gibberella zeae (Anamorph Fusarium graminearum)

Gaffoor et al.,
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824,1 Mycotoxin Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604,2

... Ab initio gene identification was accomplished using FGENESH (http://www.softberry. com) with organism-specific parameters for Neurospora crassa (12). ...


Cytokine
Volume 32, Issue 5, 7 December 2005, Pages 219-225

Expression of nine-banded armadillo (Dasypus novemcinctus) interleukin-2 in E. coli

Adams et al.,
Laboratory Research Branch National Hansen's Disease Programs, Louisiana State University, School of Veterinary Medicine, Skip Bertman Drive, Baton Rouge, LA 70803, USA

... The genomic sequence was submitted to FGENESH (http://www.softberry.com) to derive a putative cDNA and a corresponding translation for the putative amino acid ...


Comparative and Functional Genomics
Volume 6 (2005), Issue 3, Pages 138-146doi:10.1002/cfg.465

The Korea Brassica Genome Project: a Glimpse of the Brassica Genome Based on Comparative Genome Analysis With Arabidopsis

Tae-Jin Yang et al.,
1National Institute of Agricultural Biotechnology (NIAB), 224 Suinro Gwonseon-gu, Gyeonggi-do, Suwon 441–707, Korea 2Chungnam National University, Gungdong 220, Chungnam, Daejeon 305–764, Korea

... Gene annotation was achieved using several web based gene prediction programs, eg FGENE-SH Arabidopsis (http://www.softberry.com/berry. ...


Plant Molecular Biology
Volume 59, Number 1 / September, 2005, pp.191-203

Transcription Factors in Rice: A Genome-wide Comparative Analysis between Monocots and Eudicots

Xiong et al.,
(1) Present address: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China

... BGI) (Yu et al., 2002) (http://www.genomics.org.cn/) and the genes were predicted using FGENESH (Salamov and Solovyev, 2000) (http://www.softberry.com/). ...


Molecular Biology and Evolution
2005 22(10):2084-2089; doi:10.1093/molbev/msi202

MUSTANG Is a Novel Family of Domesticated Transposase Genes Found in Diverse Angiosperms

Rebecca K. Cowan, Douglas R. Hoen, Daniel J. Schoen and Thomas E. Bureau
McGill University, Biology Department, Montreal, Quebec H3A 1B1, Canada

... through AP006877 and National Center for Biotechnology Information [NCBI] accession number AE016959), predicted using FGENESH (http://www.softberry.com/berry ...


Plant Molecular Biology
Issue: Volume 57, Number 3 Date: February 2005 Pages: 445 - 460

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

Hong Yao1, 4 et al
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, 50011-3650, USA.

ABSTRACT
Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.


Nature
434, 980-986 (21 April 2005)

The genome sequence of the rice blast fungus Magnaporthe grisea

Dean et al.,
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter EX4 4QG, UK

...Gene predictions were performed using FGENESH/FGENESH1 + trained on M. grisea sequences (SoftBerry) and GENEWISE (Sanger Center) and validated against 65 characterized M. grisea genes. Additional information and gene identification...


Nature
436, 793 - 800 (11 Aug 2005)

The map-based sequence of the rice genome

International Rice Genome Sequencing Project


...the remaining centromere gaps. Annotation and bioinformatics Gene models were predicted using FGENESH (http://www.softberry.com/berry.phtml?topic = fgenesh) using the monocot trained matrix on the native and repeat-masked...


Nature Genetics
37 997 - 1002 (01 Sep 2005) Letters

Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize

Morgante et al.,
1 Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, 33100 Udine, Italy. 2 DuPont Crop Genetics Research, DuPont Experimental Station Building E353, Wilmington, Delaware 19880-353, USA.

...at http://www.girinst.org/~vladimir/RC/Data1.htm. We obtained FGENSH splicing site predictions from http://www.softberry.com/berry.phtml. Primer3 is available at http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi. Note:...


European Journal of Plant Pathology
Issue: Volume 112, Number 1 Date: May 2005 Pages: 23 - 29

Leptosphaeria maculans, a fungal pathogen of Brassica napus, secretes a subtilisin-like serine protease

Leanne M. Wilson and Barbara J. Howlett
1 School of Botany, The University of Melbourne, Parkville, Victoria, 3010, Australia

... DNA and cDNA sequences were compared to identify intron positions, which confirmed those predicted by FGENESH gene prediction software (www.softberry.com). ...


Current Genetics Issue: Volume 47, Number 5 Date: May 2005 Pages: 307 - 315

During attachment Phytophthora spores secrete proteins containing thrombospondin type 1 repeats

Andrea V. Robold1 and Adrienne R. Hardham1
(1) Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia

... info.html). The DNA sequence was searched for introns using the soft- ware program FGENESH (http://www.softberry. com/berry.phtml ...


Microbiology
151 (2005), 1499-1505

Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus

Inge A. Unsold and Shu-Ming Li
Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universitat Tubingen, Auf der Morgenstelle 8, 72076 Tubingen, Germany

... FGENESH (Softberry; www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used for intron prediction ...


Eukaryotic Cell
March 2005, p. 526-535, Vol. 4, No. 3

Sex-Specific Homeodomain Proteins Sxi1a and Sxi2a Coordinately Regulate Sexual Development in Cryptococcus neoformans

Christina M. Hull,1, Marie-Josee Boily,1 and Joseph Heitman1,2*
Department of Molecular Genetics and Microbiology,1 the Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina2

... Sequence manipulations. Splice predictions of candidate gene sequences for SXI2a were facilitated with a Softberry algorithm (www.softberry.com). ...


New Phytologist
167 (1), July 2005, 239-247.

Identification of perennial ryegrass (Lolium perenne (L.)) and meadow fescue (Festuca pratensis (Huds.)) candidate orthologous sequences to the rice Hd1(Se1) and barley HvCO1 CONSTANS-like genes through comparative mapping and microsynteny

P. Armstead, L. Skot, L. B. Turner, K. Skot, I. S. Donnison, M. O. Humphreys and I. P. King

... Predictions of mRNA and protein sequences were carried out using FGENESH and FGENESH+ software ( http:/ / www.softberry.com/ berry.phtml ). ...


Plant Physiology
May 2005, Vol. 138, pp. 38-46

BIOINFORMATICS-PLANT DATABASES
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome1

Steven B. Cannon et al
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (S.B.C., X.W., E.K.S.C., J.V., J.M., N.D.Y.)

... Annotation involves a multi-institution pipeline, relying on Medicago-trained FGENESH (Salamov and Solovyev, 2000 ) predictions, the EuGene (Foissac et al ...


Plant Physiology
May 2005, Vol. 138, pp. 18-26

BIOINFORMATICS-PLANT DATABASES
The Institute for Genomic Research Osa1 Rice Genome Annotation Database1

Qiaoping Yuan et al
The Institute for Genomic Research, Rockville, Maryland 20850

... The ab initio gene finders used in the rice EGC pipeline include FGENESH (monocot matrix; Salamov and Solovyev, 2000 ), GeneMark.hmm (rice matrix; Lukashin and ...


Genome Research
15:577-582, 2005

Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions

Chaochun Wei1 et al.
1 Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA

... Finally, we compared TWINSCAN with two other gene-prediction systems that have recently been developed for nematodes-FGENESH (Salamov and Solovyev 2000 ...


Plant Physiology
April 2005, Vol. 137, pp. 1174-1181

UPDATE ON SEQUENCING MEDICAGO TRUNCATULA AND LOTUS JAPONICUS
Sequencing the Genespaces of Medicago truncatula and Lotus japonicus1

Nevin D. Young et al
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (N.D.Y., S.B.C.)

... (These estimates are based on FGENESH predictions [Salamov and Solovyev, 2000] using a Mt-trained matrix, retaining peptides with a BLASTP match at 10e-4 to the UniProt NREF100 database of peptides [Apweiler et al., 2004]. This estimate for Lj differs from the published value of 1 gene per 10.1 kb [Asamizu et al., 2003a] due to the use here of the FGENESH gene-calling algorithm so Mt and Lj could be compared directly.)...
...This estimate increases to 6,500 when Lj genes are predicted by the Mt-trained FGENESH algorithm described earlier...


International Journal of Cancer
Volume 109, Issue 1 , Pages 71 - 75

Candidate regions of tumor suppressor locus on chromosome 9q31.1 in gastric cancer

Naoto Kakinuma 1 et al
1Novartis Pharma Tsukuba Research Institute, Ibaraki, Japan
2Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
3Second Department of Surgery, Gunma University School of Medicine, Gunma, Japan

... predict the genes between D9S277 and D9S127 in 9q31.1, the gene prediction tools also in the UCSC Genome Browser having Acembly, Ensembl, FGENESH , GenScan and ...


Genome Research
15:54-66, 2005

Gene and alternative splicing annotation with AIR

Liliana Florea1,4,5 et al
1 Informatics Research, Applied Biosystems, Rockville, Maryland 20850, USA;

... Ab initio prediction programs such as GenScan (Burge and Karlin 1997 ), FGENESH (Salamov and Solovyev 2000 ), Genie (Kulp et al. ...


Nucleic Acids Research
2005, Vol. 33, Database issue D399-D402

SilkDB: a knowledgebase for silkworm biology and genomics

Jing Wang1 et al
1 College of Life Sciences, Peking University, Beijing 100871, China,

... BGF is a self-developed ab initio program based on GenScan (9) and FGENESH (10), and was successfully utilized for our rice genome annotation (11). ...


Clinical Cancer Research
Vol. 11, 4029-4036, June 1, 2005

A Molecular Signature in Superficial Bladder Carcinoma Predicts Clinical Outcome

Lars Dyrskjot1 et al
Authors' Affiliations: 1 Molecular Diagnostic Laboratory, Department of Clinical Biochemistry

... array comprising 59,619 probe sets representing 46,000 unique sequences, including known genes, expressed sequence tag clusters, and FGENESH-predicted exons ...


BMC Evolutionary Biology
2005, 5:1

The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants

Yuanji Zhang* and Liangjiang Wang
Address: Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA

... Despite minor differences in the gene structure prediction, both gene prediction programs FGENESH and GENSCAN agree on the major features of the protein ...


PLoS Biol.
2005 June; 3(6): e181.

RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons

Vladimir V Kapitonov1 and Jerzy Jurka1
1Genetic Information Research Institute, Mountain View, California, United States of America David Nemazee, Academic Editor

... Using FGENESH [33], we detected that the RAG1 core-like open reading frame (ORF) in the contig 29068 forms a terminal exon (positions 1154-2947) of an ...


Genetics
Published Articles Ahead of Print, published on February 16, 2005 as 0.1534/genetics.104.036327

Identification and Characterization of Regions of the Rice Genome Associated with Broad- Spectrum, Quantitative Disease Resistance

Randall J. Wisser R.J * et al.
*Department of Plant Breeding and Genetics, Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853

... GENSCAN (B URGE and K ARLIN 1997) and FGENESH (S ALAMOV and S OLOVYEV 2001) to predict open reading frames. Further searches against ...


Plant Physiology
January 2005, Vol. 137, pp. 176-189

Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells1,[w]

Zhen Xie2 et al
Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154

... First of all, three genes (OsWRKY41, -43, and -44) were reannotated using FGENESH (www.softberry.com), because the first introns of these genes were too small ...


PLoS Biol
3(6): e181 (2005)

RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons.

Vladimir V. Kapitonov1*, Jerzy Jurka1*
1 Genetic Information Research Institute, Mountain View, California, United States of America

... Using FGENESH [33], we detected that the RAG1 core-like open reading frame (ORF) in the contig 29068 forms a terminal exon (positions 1154-2947) of an ...


Plant and Cell Physiology 2005 46(1):3-13; doi:10.1093/pcp/pci503

From Mapping to Sequencing, Post-sequencing and Beyond

Takuji Sasaki1, Takashi Matsumoto, Baltazar A. Antonio and Yoshiaki Nagamura
National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

... The gene predictions by programs such as Genescan (Burge and Karlin 1997 ), FGENESH [see Appendix 1 (4)] and Genemark [see Appendix 1 (5)], BLAST (Altschul et ...


Nature Biotechnology, 2005


Improving the nutritional value of Golden Rice through increased pro-vitamin A content

JA Paine, CA Shipton, S Chaggar, RM Howells, MJ ...

... Arabidopsis thaliana psy and rice psy (AY024351) genes identified genomic sequences of similarity in which genes were predicted using FGENESH algorithm with ...


Genetics
Published Articles Ahead of Print, published on January 16, 2005 as 10.1534/genetics.104.035543

THE GENETIC BASIS FOR INFLORESCENCE VARIATION BETWEEN FOXTAIL AND GREEN MILLET (POACEAE)

Andrew N. Doust*, Katrien M. Devos1, Mike D. Gadberry*, Mike D. Gale, & Elizabeth A. Kellogg*
*University of Missouri-St. Louis, Department of Biology, One University Boulevard, St. Louis, MO 63121, USA

... Each of these contigs was scanned using FGENESH (S ALAMOV and S OLOVYEV 2000), and open reading frames (ORFs) were translated and ...


PLoS Biol
3(1): e13 January 2005

Sorghum Genome Sequencing by Methylation Filtration

Joseph A. Bedell et al.
Bioinformatics, Orion Genomics, Saint Louis, Missouri, United States of America,

... additional parameters: wordmask=seg; lcmask; M=1; N=-1; Q=3; R=3; kap; E=1e-10; hspmax=0. To look for potentially novel genes, we used FGENESH (http://www ...


BMC Genomics
2005, 6:11 doi:10.1186/1471-2164-6-11

FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells

Demet Nalbant et al.
Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA

... These results were compared against genes assembled by two gene prediction programs, FGENESH: http://www.softberry.com/berry.phtml and GENSCAN: http://genes.mit ...


Plant Physiology
July 2005, Vol. 138, pp. 1205-1215

Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus1,[w]

Romain Guyot et al.
Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland (R.G., E.S., B.K., H.-Q.L.); and Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China (X.C., Y.S., Z.C., H.-Q.L.)

... Putative genes were determined by a combination of coding region prediction software (GENSCAN, FGENESH, and MZEF with Arabidopsis and/or monocot matrix ...


J Gen Virol
86 (2005), 973-983; DOI 10.1099/vir.0.80833-0

Cloning, characterization and analysis by RNA interference of various genes of the Chelonus inanitus polydnavirus

Marianne Bonvin et al
Institute of Cell Biology, University of Berne, Baltzerstrasse 4, CH-3012 Bern, Switzerland

... 12g1forw (5'-GAGTCCATGCCGAATGTCAC-3') and 12g1rev (5'-CTTCTTGCACAGCGACGAAC-3') were set to amplify the middle region of 12g1, as predicted with FGENESH 1.0 and ...


BMC Plant Biol.
2005, 5:15

Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana

Mudge et al.,
1Dept of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108 USA

... Genes were predicted in G. max and M. truncatula genomic sequences using the dicot (Arabidopsis) matrix of FGENESH [59,60]http://www.softberry.com webcite. ...


PNAS
February 1, 2005 vol. 102 no. 5 1566-1571

A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome

Mark Yandell et al
Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200; and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720

... genes, based on a microarray-based approach that involved hybridizing randomly primed cDNA against probes corresponding to a large set of FGENESH predictions. ...


Insect Molecular Biology
Volume 14 Issue 2 Page 113 - 119 April 2005

Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence

X.-F. Zha et al
Correspondence: Dr Qing-You Xia, The Key Sericultural Laboratory of Agricultural Ministry, Southwest Agricultural University, Chongqing 400716, China.

... previously predicted silkworm genes in the genomic sequences by BGF, a newly developed program based on GENSCAN (Burge & Karlin, 1997) and FGENESH (Salamov & ...


Microbiology
151 (2005), 2199-2207; DOI 10.1099/mic.0.27962-0

Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus

Alexander Grundmann and Shu-Ming Li
Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universitat Tubingen, Auf der Morgenstelle 8, 72076 Tubingen, Germany

... FGENESH (Softberry, Inc., http://www.softberry.com/berry.phtml) and the DNASIS software package (version 2.1; Hitachi Software Engineering) were used for ...


FGENESH 2002-2004

Fungal Genetics and Biology
Volume 41, Issue 1, January 2004, Pages 23-32

Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses

Brandi L Kutil a, Gang Liu a, 1, Julia Vrebalov b and Heather H Wilkinson
aDepartment of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77845-2132, USA bBoyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801, USA

... Contigs were also submitted to FGENESH (http://www.softberry.com/berry.phtml) to predict ORFs using N. crassa as the training set. ...


Eukaryotic Cell
April 2004, p. 420-429, Vol. 3, No. 2

Cryptococcus neoformans Virulence Gene Discovery through Insertional Mutagenesis

Alexander Idnurm, Jennifer L. Reedy, Jesse C. Nussbaum, and Joseph Heitman
Department of Molecular Genetics and Microbiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710

... FGENESH software (SoftBerry) was used to search for coding regions within the sequence, and BLAST searches were conducted against the GenBank database to infer ...


Breeding Science
Vol. 54 (2004) , No. 2 165-175

Molecular Characterization of a 313-kb Genomic Region Containing the Self-incompatibility Locus of Ipomoea trifida, a Diploid Relative of Sweet Potato

Rubens Norio Tomita et al.,
1) Faculty of Bioresources, Mie University 2) Division of Natural Science, Osaka Kyoiku University 3) Life Science Research Center, Mie University

... gatech.edu/GeneMark), GENE- SCAN (http://genes.mit.edu/GENESCAN), GlimmerM (http:// www.tigr.org/tdb.glimmerm/glmr) and FGENESH (http:// softberry.com/berry ...


J. Biol. Chem
Vol. 279, Issue 18, 18550-18558, April 30, 2004

The Two-pore Domain K+ Channel, TRESK, Is Activated by the Cytoplasmic Calcium Signal through Calcineurin

Gabor Czirjak, Zsuzsanna E. Toth, and Peter Enyedi
From the Department of Physiology and Laboratory of Neuromorphology, Semmelweis University, H-1444 Budapest, Hungary

... The conceptual coding region of the new channel was calculated from the neighboring genomic sequences by the FGENESH program at the Softberry site on the World ...


Genome Res.
2004. 14: 1916-1923 doi: 10.1101/gr.2332504

Close Split of Sorghum and Maize Genome Progenitors

Swigonova et al.,
1Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA 2Department of Biological Sciences and Genetics Program, West Lafayette, Indiana 47907, USA

... Genes predicted by FGENESH (www.softberry.com) and GENSCAN (http://genes.mit.edu/ GENSCAN.html) programs were further analyzed by homology searches using BLAST ...


PNAS
October 26, 2004 vol. 101 no. 43 15289-15294

Estimating genome conservation between crop and model legume species

Choi et al.,
Department of Plant Pathology and §College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616; ¶Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108

... NCBI (18). Ab initio gene prediction involved the eudicot version of fgenesh (www.softberry.com/berry.phtml?topic=gfind). Gene prediction ...


PNAS
January 20, 2004 vol. 101 no. 3 700-707

Pattern of diversity in the genomic region near the maize domestication gene tb1

Richard M. Clark†, Eric Linton‡,§, Joachim Messing‡, and John F. Doebley†
†Laboratory of Genetics, University of Wisconsin, Madison, WI 53706; and ‡Waksman Institute, Rutgers University, Piscataway, NJ 08854

... default" and DNA source set to "Grasses." Nonrepetitive DNA was analyzed for genes by using the fgenesh gene prediction software (www.softberry.com/berry ...


Eukaryotic Cell
October 2004, p. 1088-1100, Vol. 3, No. 5

Introns and Splicing Elements of Five Diverse Fungi

Kupfer et al.,
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City,2 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma,1

... Translation of the DNA sequences was done by using FGENSH at the Softberry website (http://www.softberry.com/) with either the S. pombe or the N. crassa matrix ...


Journal of Experimental Biology
207, 4573-4586 (2004)

Functional characterisation of the Anopheles leucokinins and their cognate G-protein coupled receptor

Jonathan C. Radford, Selim Terhzaz, Pablo Cabrero, Shireen-A. Davies and Julian A. T. Dow
Institute of Biomedical and Life Sciences, Division of Molecular Genetics, University of Glasgow, Glasgow G11 6NU, UK

... This region plus the surrounding 20 kb of genomic sequence either side was then analysed with the Softberry FgenesH gene prediction program (www.softberry.com ...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 4 Date: August 2004 Pages: 681 - 689

Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm

Mark Jung et al
(1) DuPont Crop Genetics, Experimental Station, P.O. Box 80353, Wilmington, DE 19880-0353, USA

... 1). Gene locations were defined by several methods. Annotations provided in Tikhonov et al. (1999) were first used, then FGENESH gene-finding software ...


DNA Sequence - The Journal of Sequencing and Mapping
Issue: Volume 15, Number 4 / August, 2004 Pages: 269 - 276

Isolation, Characterization and Expression Analysis of a Leaf-specific Phosphoenolpyruvate Carboxylase Gene in Oryza sativa

Chang-Fa Lin et al
State Key Laboratory of Genetic Engineering Institute of Genetics, School of Life Sciences, Fudan University Shanghai 200433 P.R.China

... tools of GeneMark (http://opal. biology.gatech.edu/geneMark/) and Softberry (http://www.softberry.com). For the isolation of putative ...


Nature Genetics
36, 40 - 45 (01 Jan 2004)

Complete sequencing and characterization of 21,243 full-length human cDNAs

Ota et al.


...PSORT II, http://psort.ims.u-tokyo.ac.jp/; DIGIT, http://digit.ims.u-tokyo.ac.jp; FGENESH, http://www.softberry.com/berry.phtml; GENSCAN, http://genes.mit.edu/GENSCAN.html; HMMGENES, http://www.cbs.dtu.dk/services/HMMgene/; HUNT...


Plant Molecular Biology
Issue: Volume 54, Number 4 Date: March 2004 Pages: 519 - 532

Genome-Wide Analysis of the GRAS Gene Family in Rice and Arabidopsis

Chaoguang Tian1, Ping Wan1, Shouhong Sun1, Jiayang Li1 and Mingsheng Chen1*
(1) Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China

... database. FGENESH (Salamov and 90 Solovyev, 2000) was used for gene prediction. ... pre- 207 dicted by FGENESH (minor discrepancies exist due 208 ...


Mycological Research
(2004), 108: 853-857 Cambridge University Press

Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes

Andrew H. SIMS a1, Manda E. GENT a1, Geoffrey D. ROBSON a1, Nigel S. DUNN-COLEMAN a2 and Stephen G. OLIVER a1c1
a1 School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

... Kingdom. Page 2. Genewise, FGENESH, FGENESH+) consisting of 9541 putative open reading frames (ORFs) was released in June 2003. We ...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 1 Date: June 2004 Pages: 129 - 139

Gene content and density in banana (Musa acuminata) as revealed by genomic sequencing of BAC clones

R. Aert1, 2, L. Sagi2 and G. Volckaert1
(1) Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium Present address: Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, (2) Kasteelpark Arenberg 13, 3001 Leuven, Belgium

... gsc.riken.go.jp), FGENESH version 1.1 (Salamov and Solovyev 2000; http://www.softberry. com), genemark.hmm version 2.2a (Lukashin and Borodovsky 1998; http ... Genome Research 14:2503-2509, 2004


EAnnot: A genome annotation tool using experimental evidence


Li Ding et al
Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63110, USA

...Some ab initio programs, such as Genscan (Burge and Karlin 1997 ) and FGENESH (Salamov and Solovyev 2000 ) are based on intrinsic characteristics of coding sequence (e.g., codon usage, consensus splice sites, etc.) and require training on known genes from the organism...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 7 Date: November 2004 Pages: 1434 - 1447

Full-genome analysis of resistance gene homologues in rice

B. Monosi1, R. J. Wisser2, L. Pennill1 and S. H. Hulbert1
(1) Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
(2) Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA


... DNA sequences were analyzed using the gene prediction programs GENSCAN (Burge and Karlin 1997; http://genes.mit.edu/GENSCAN.html) and FGENESH (Salamov and ...


arXiv:q-bio.GN/0402046 v1 27 Feb 2004


Sublinear growth of Information in DNA sequences

Giulia Menconi
Dipartimento di Matematica Applicata and C.I.S.S.C. Centro Interdisciplinare per lo Studio dei Sistemi Complessi Universit`a di Pisa Via Bonanno Pisano 25/b 56126 PISA - Italy

...As a result, four putative genes G1, G2, G3 and G4 have been located by means of Hidden Markov Model-based program FGENESH2 that has been created for predicting multiple genes and their structure in genomic DNA sequences. The analysis via FGENESH has been exploited with respect to known genes in Arabidopsis thaliana. Their predicted position is illustrated in Figure 13. ...2This program is available at the website www.softberry.com to which we refer con-cerning the reliability and e_ciency of the algorithm....


Current Opinion in Plant Biology
2004, 7:732-736

Consistent over-estimation of gene number in complex plant genomes

Jeffrey L Bennetzen1,4, Craig Coleman2,7, Renyi Liu1,5, Jianxin Ma1,6 and Wusirika Ramakrishna3,8
1 Department of Genetics, University of Georgia, Athens, Georgia 30602, USA

...We have found that the standard gene-discovery programs FGENESH, GeneMark and GENSCAN annotate segments of most retrotransposons and many invertedrepeat transposable elements as genes. Using FGENESH to annotate maize BAC clones, for instance, 70-100% of the predicted genes are actually from transposable elements...


The Plant Cell
16:2795-2808 (2004)

Spotted leaf11, a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activity

Li-Rong Zeng et al
a Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210

... in spl11. Exons predicted in G3 by the programs GENSCAN and FGENESH using different matrixes are displayed in dark gray. (D) RFLP ...


Human Genomics,
Volume 1, Number 2, January 2004, pp. 146-149(4)

The truth about mouse, human, worms and yeast

Authors: David R. Nelson1; Daniel W. Nebert2
1: Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA 2: Department of Environmental Health and Center for Environmental Genetics (CEG), University of Cincinnati Medical Center, Cincinnati, Ohio 45267-0056, USA

... unpublished data, 2003; see also Ref. [7]), FGENESH, 21 TWINSCAN 22 and the Ensembl annotation pipeline. 23 The output of the four ...


Genome Biology
2004, 5:R73 doi:10.1186/gb-2004-5-10-r73

A comprehensive transcript index of the human genome generated using microarrays and computational approaches

Eric E Schadt et al
1Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA

...GrailEXP 4.0 [47], GENSCAN 1.0 [48], FGENESH [49], and FGENESH+ [49]ab initio gene-prediction algorithms were run independently across the entire genome assembly to augment alignment-based gene identification methods...


Genome Research
14:988-995, 2004

GeneWise and Genomewise

Ewan Birney1,3, Michele Clamp2 and Richard Durbin2
1 The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; 2 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK


...There has been a long history of successful ab initio programs which do not use any additional evidence to predict genes on genomic DNA, of which Genscan (Burge and Karlin 1997 ) and FGENESH (Solovyev and Salamov 1997 ) are two of the most successful cases....
...Another class of evidence-based gene prediction programs are ones which use external evidence to influence the scoring of potential exons, including SGP-2 (Parra et al. 2003 ), Genie (Kulp et al. 1996 ), Genomescan (Yeh et al. 2001 ), HMMGene (Krogh 2000 ), and FGENESH++ (Solovyev and Salamov 1997 )...


PNAS
February 17, 2004 vol. 101 no. 7 1910-1915

Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms

Jongmin Nam et al
Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802

...Because annotation of rice gene was still in progress at the time of this study, we ourselves conducted gene annotation by using the computer program FGENESH (www.softberry.com) from the genome sequences obtained from TIGR and the Rice Genome Database (China) (25).


Functional & Integrative Genomics
Issue: Volume 4, Number 2 Date: May 2004 Pages: 102 - 117

Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny

Nagendra K. Singh et al.,
Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

... Wherever RiceGAAS data were not available, the genes were predicted by FGENESH trained for monocot plant species (http:// www.softberry.com/berry.phtml). ...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 1 Date: June 2004 Pages: 10 - 22

Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements

M. Lescot et al
1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, 9052 Gent, Belgium

... 1999; http://www.tigr.org/tdb/glimmerm/glmr_form.html), and FGENESH for dicots or monocots (Salamov and Solovyev 2000; http://www.softberry.com/). ...


BIOINFORMATICS,
2004 vol.20 N.9 p.1416-1427
J Yuan, B Bush, A Elbrecht, Y Liu, T Zhang, W Zhao ... -

... suchasGRAIL(Lopezetal., 1994; Roberts, 1991; Uberbacher et al., 1996), GENESCOPE (Murakami and Takagi, 1998), FGENESH (Salamov and Solovyev, 2000), GeneMark ...


Molecular Plant Pathology
Volume 5 Issue 6 Page 515 - November 2004

Heading for disaster: Fusarium graminearum on cereal crops

RUBELLA S. GOSWAMI AND H. CORBY KISTLER

... This pipeline uses a combination of the programs FGENESH and FGENESH+ (Salamov and Solovyev, 2000) modified by Softberry ( http:/ / www.softberry.com ) with ...


Nucleic Acids Research
2004, Vol. 32, Database issue D41-D44

MIPS: analysis and annotation of proteins from whole genomes

H. W. Mewes et al
1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany and 2 Technische Universitat Munchen, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany

... The genome of 40 Mb encodes 10 000 proteins automatically predicted by the program FGENESH (http://softberry. com), specifically trained for Neurospora. ...


Annual Review of Genomics and Human Genetics
Vol. 5: 15-56 (Volume publication date September 2004)

COMPARATIVE GENOMICS


Webb Miller, Kateryna D. Makova, Anton Nekrutenko, and Ross C. Hardison
The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, and the Departments of Biology, Computer Science and Engineering, and Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania

... These algorithms include Genscan, the most popular gene prediction tool (24), GenMark (117), FGENESH (155), GeneID (144), and others (for an excellent overview ...


DNA and Cell Biology
May 2004, Vol. 23, No. 5: 311-324

Harbinger Transposons and an Ancient HARBI1 Gene Derived from a Transposase

Vladimir V. Kapitonov , Jerzy Jurka
Genetic Information Research Institute, Mountain View, California.

... We used FGENESH (Salamov and Solovyev, 2000) and GeneScan (Burge and Karlin, 1997) for the identification of exons and introns. The d N /d S ratio, ...


Nucleic Acids Research
2004, Vol. 32, Database issue D377-D382

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

Wenming Zhao et al
1 Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China

... The contig sequences were annotated for gene content by using automated processes that involve ab initio gene finders, such as FGENESH (http://www.softberry.com ...


Genome Research
14:1932-1937, 2004

Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome

Jinsheng Lai et al
1 Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA;

... A total of 54,397 putative genes could be predicted for the rice genome from this data set (Table 3) using the FGENESH program with the default setting for ...


Plant Molecular Biology
Issue: Volume 54, Number 1 Date: January 2004 Pages: 55 - 69

Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat

Xiu-Ying Kong1, 2, Yong Qiang Gu3, Frank M. You4, Jorge Dubcovsky4 and Olin D. Anderson3
1. Genetic Resources Conservation Program, University of California, Davis, CA 95616, USA
2. Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
3. U.S. Dept. of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710, USA
4. Department of Agronomy and Range Sciences, University of California, Davis, CA 95616, USA

... FGENESH (http://www.softberry.com/berry.phtml) and GENES- CAN (http://genemark. mit.edu/GENESCAN.html) were used for gene prediction. ...


Current Genetics
Issue: Volume 44, Number 6 Date: January 2004 Pages: 329 - 338

Chromosome rearrangements in isolates that escape from het-c heterokaryon incompatibility in Neurospora crassa

Qijun Xiang1 and N. Louise Glass1
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA

... Hypothetical proteins are predicted from FGENESH calls with overlapping Blastx hits (but not with trusted homology), while Predicted ...


Molecular Genetics and Genomics
Issue: Volume 271, Number 4 Date: May 2004 Pages: 402 - 415

Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes

T. Zhou et al
1. State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093 Nanjing, China

... to 5000-10,000 bp from both ends of the hits, and then the expanded nucleotide fragments were reannotated using the gene-finding programs FGENESH (http:// www ...


Proc Natl Acad Sci U S A.
2004 June 15; 101(24): 9045-9050.

Genetic control of branching in foxtail millet

Andrew N. Doust et al
*Department of Biology, University of Missouri, 8001 Natural Bridge Road, St Louis, MO 63121; and ‡John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom

... Each of these contigs was scanned by using FGENESH (28), and identified ORFs were translated and compared with ORFs from other contigs from the same QTL region ...


Mol. Biol. Evol.
21(9):1769-1780. 2004

Merlin, a New Superfamily of DNA Transposons Identified in Diverse Animal Genomes and Related to Bacterial IS1016 Insertion Sequences

Cedric Feschotte1
Departments of Plant Biology and Genetics, The University of Georgia, Athens

... coding sequences were assembled by removing introns predicted with more than 85% confidence by NetGene2 (http://www.cbs.dtu.dk) and/or FGENESH (http://genomic ...


Genome Research
14:1924-1931 ©2004

Gene Loss and Movement in the Maize Genome

Jinsheng Lai et al
1Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA; 2Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA

... The FGENESH program predicted four, of which three (gene 1d in the maize orp1 region; gene 5a, 5b in the rice r1 region) would produce truncated proteins ...


Internal Medicine Journal
Volume 34 Issue 3 Page 79 -90 - March 2004

Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes

H. Kiyosawa et al
Affiliations: 1Technology and Development team for Mammalian Cellular Dynamics, Bioresource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki

...Page 1. Internal Medicine Journal 2004; 34: 79-90. O RIGINAL A RTICLE. Systematic genome-wide approach to positional candidate. cloning ...


Molecular Microbiology
Volume 54 Issue 2 Page 407 - October 2004

Cryptococcus neoformans Kin1 protein kinase homologue, identified through a Caenorhabditis elegans screen, promotes virulence in mammals

Eleftherios Mylonakis et al
1Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA.

... Sequences were compared with the H99 genome database at Duke University, and genes predicted in these regions by FGENESH software ( http:/ / www.softberry.com ...


TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 5 Date: March 2004 Pages: 903 - 913

Characterization of soybean genomic features by analysis of its expressed sequence tags

Ai-Guo Tian et al
1. Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101 Beijing, China

... six BAC-contig sequences of M. truncatula were analyzed and the results based on the gene prediction program FGENSH (Arabidopsis match/FGENESH prediction) (http ...


Current Proteomics,
Volume 1, Number 1, January 2004, pp. 41-48(8)

Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins

McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK

... The polymorphic 'hypothetical transcriptome' was cons- tructed from transcripts predicted by FGENES, FGENESH (Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...


Chinese Science Bulletin
2004 Vol. 49 No. 4 355-362

The VER2 promoter contains repeated sequences and requires vernalization for its activity in winter wheat (Triticum aestivum L.)

XU Wenzhong et al
1. Research Center for Molecular Developmental Biology, Key Lab of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing 100093, China;

... Sequence analyses were finished using biological softwares on Internet, such as FGENESH 1.0 (Prediction of potential genes in Plant (Dct) genomic DNA). ...


TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 3 Date: February 2004 Pages: 392 - 400

Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice

Can Li1, Yu Zhang1, Kai Ying1, Xiaolei Liang1 and Bin Han1
(1) National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China

... To characterize the possible relationship between SSRs and genes predicted by using FGENESH, we investigated the distribution of SSRs in the rice chromosome-4 ...


Proc Natl Acad Sci U S A.
2004 June 29; 101(26): 9885-9890.

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Kelly Palaisa,* Michele Morgante, Scott Tingey, and Antoni Rafalski*
DuPont Crop Genetics, Molecular Genetics Group, 1 Innovation Way, Newark, DE 19711; *Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716

... The Y1 gene comprises a small uninterrupted gene island consisting of the Y1, an MLO homolog lying immediately downstream of Y1, and an FGENESH-predicted gene ...


TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 8 Date: May 2004 Pages: 1449 - 1457

Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein

H. Akagi et al
1. Laboratory of Plant Breeding and Genetics, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Kaidoubata-Nishi 241-7, Shimoshinjyo-Nakano, 010-0195 Akita, Japan

... Software Develop- ment, Tokyo). Genomic sequences were also analyzed using gene prediction programs, genescan and FGENESH. Table 1 DNA ...


Genome Research
14:942-950, 2004

The Ensembl Automatic Gene Annotation System

Val Curwen et al
1 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; 2 EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; 3 The Broad Institute, Cambridge, Massachusetts 02141, USA

... Commonly, we use Genscan for ab initio prediction in human, mouse, and rat, but the system is equally applicable to other methods such as FGENESH (Solovyev et ...


Gene
324 (2004) 105-115

Transcript abundance of rml1, encoding a putative GT1-like factor in rice, is up-regulated by Magnaporthe grisea and down-regulated by light

Rong Wang a,b, Guofan Honga,b, Bin Hana,*
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China

... 1A and 2A). The structure of rml1 _ a is as same as that predicted by FGENESH software. The 3V UTR of rml1 _ a is confirmed with the length of 596 bp. ...


Genome Biology
2004, 5:R46 doi:10.1186/gb-2004-5-7-r46

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. Indica

Cizhong Jiang1, Xun Gu1, 2 and Thomas Peterson1
1Department of Genetics, Development and Cell Biology, and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
2LHB Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA

... FGENESH has been used successfully to predict genes in rice [9], and GenScan was used together with it to predict genes by taking rice genomic sequences as ...


Molecular Microbiology
53 (5), 1307-1318. - September 2004

The sirodesmin biosynthetic gene cluster of the plant pathogenic fungus Leptosphaeria maculans

Donald M. Gardiner et al
1School of Botany, The University of Melbourne, Victoria, Australia 3010.

... http:/ / www.tigr.org . Putative genes were predicted using FGENESH software at http:/ / www.softberry.com. Fungal culture. The wild type ...


Journal of Molecular Evolution
Issue: Volume 59, Number 6 Date: December 2004 Pages: 761 - 770

Analysis of the Molecular Evolutionary History of the Ascorbate Peroxidase Gene Family: Inferences from the Rice Genome

Felipe Karam Teixeira1, Larissa Menezes-Benavente1, Rogerio Margis1, 2 and Marcia Margis-Pinheiro1
(1) Laboratorio de Genetica Molecular Vegetal, Departamento de Genetica, UFRJ, 21944-970 Rio de Janeiro, Brasil
(2) Departamento de Bioquimica, Instituto de Quimica, UFRJ, 21944-970 Rio de Janeiro, Brasil

... Genomic se- quences were also analyzed in the FGENESH gene structure pre- diction program (http://www.softberry.com/) (Solovyev 2001) and GeneMark program (http ...


Journal of Biotechnology
109 (2004) 217-226

Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap

Xiaohui Liu et al
A National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China

... ers. These sequences were further annotated using gene-prediction software FGENESH to give the pos- sible protein-coding region. ...


Science
2004, 303: 1364-1367.

Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes

Ane et al. (2004).

... 17. HK Choi et al., Genetics, in press. 18. FGENESH, see www.softberry.com/berry. phtml. 19. E. Bornberg-Bauer, E. Rivals, M. Vingron, Nucleic Acids Res. ...


Proc Natl Acad Sci U S A.
2004 August 24; 101(34): 12404-12410.

Inaugural Articles
Rapid recent growth and divergence of rice nuclear genomes

Jianxin Ma and Jeffrey L. Bennetzen*
Department of Genetics, University of Georgia, Athens, GA 30602

... Almost all LTR-retrotransposons, including solo LTRs, identified in our studies were predicted as genes by the gene-finding program FGENESH (data not shown). ...


The Plant Journal
Volume 37 Issue 4 Page 517 -527 - February 2004

Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein

Xinli Sun, Yinglong Cao, Zhifen Yang, Caiguo Xu, Xianghua Li, Shiping Wang* and Qifa Zhang
National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, China

... al., 1997). Gene prediction programs used were genscan (Burge and Karlin, 1997) and FGENESH (http://www.softberry.com). Promoter ...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 3 Date: August 2004 Pages: 515 - 522

Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice

K. Saito1 , Y. Hayano-Saito1, W. Maruyama-Funatsuki1, Y. Sato1 and A. Kato1
(1) National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1 , Toyohira, Sapporo, Hokkaido, 062-8555, Japan

... GENSCAN , RICEHMM , FGENESH , MZEF ), a splice prediction program ( SPLICEPREDIC- TOR ), homology search analysis programs ( BLAST , HMMER , ...


TAG Theoretical and Applied Genetics
Issue: Volume 109, Number 4 Date: August 2004 Pages: 690 - 699

The anthracnose resistance locus Co-4 of common bean is located on chromosome 3 and contains putative disease resistance-related genes

M. Melotto1, 4 , M. F. Coelho1, A. Pedrosa-Harand2, J. D. Kelly3 and L. E. A. Camargo1
1. Departamento de Fitopatologia, Laboratorio de Genetica Molecular, ESALQ, Universidade de Sao Paulo, Piracicaba, SP, C.P. 9, 13418-900, Brazil

... and Karlin 1997; http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www. softberry.com/)-using Arabidopsis as the model or- ganism. ...


Journal of Genetics,
Vol. 83, No. 1, P. 79-99, April 2004

Structural and functional analysis of rice genome

Tyagi A. K. et al
Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India

... It inte- grates results from several gene prediction software such as GENSCAN (Burge and Karlin 1997), FGENESH (Sala- mov and Solovyev 2000), RiceHMM (Sakata ...


The Plant Cell
16:1220-1234 (2004)

Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice

Shin-Han Shiua, et al
a Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

... a permissive E value cutoff of 1. The rice genes from the indica subspecies was predicted using the whole genome shotgun assembly with FGENESH (Solovyev, 2002 ...


Genome Research
14:1474-1482 (2004) © by Cold Spring Harbor Laboratory Press ISSN 1088-9051/04;

Incongruent Patterns of Local and Global Genome Size Evolution in Cotton

Corrinne E. Grover,1 HyeRan Kim,2 Rod A. Wing,2 Andrew H. Paterson,3 and Jonathan F. Wendel1,4
1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA; 2Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA; 3Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA

... Potential genes were predicted by three independent programs: FGENESH (http://www.softberry.com/), ...


Plant Physiology,
May 2004, Vol. 135, pp. 459-470

Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four Triticeae Genomes

Yong Qiang Gu*, Devin Coleman-Derr, Xiuying Kong and Olin D. Anderson
United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710 (Y.Q.G., D.C.-D., O.D.A.); and Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing 100081 China (X.K.)
... FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark. mit.edu/GENESCAN.htm) were used for gene prediction. ...


Plant Physiology,
October 2004, Vol. 136, pp. 3177-3190

Comparative Sequence Analysis of the Region Harboring the Hardness Locus in Barley and Its Colinear Region in Rice1

Katherine S. Caldwell2, Peter Langridge and Wayne Powell*
Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (K.S.C., W.P.); and School of Agriculture and Wine (K.S.C., P.L.) and Australian Centre for Plant Functional Genomics (P.L.), University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia

... jp/; Sakata et al., 2002 ), which couples the integration of several programs for the prediction of open reading frames (GENSCAN, RiceHMM, FGENESH, MZEF) with ...


GENES & DEVELOPMENT
18:687-699, 2004

pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos

Angelike Stathopoulos1, Bergin Tam1, Matthew Ronshaugen1, Manfred Frasch2 and Michael Levine1
1 Department of Molecular and Cell Biology, Division of Genetics & Development, University of California, Berkeley, California 94720-3204, USA; 2 Brookdale Department of Molecular Cell and Developmental Biology, Mount Sinai School of Medicine, New York, New York 10029, USA

... FGF protein sequences used in alignment and phylogenetic reconstruction were gathered from GenBank or inferred from genomic sequence using GENESCAN (Burge and Karlin 1997) and FGENESH...


Genome Research
14:1888-1901, 2004

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

Ann-Marie Mallon et al
1 Medical Research Council Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom; 2 Wellcome Trust Sanger Institute, Hinxton Genome Campus, United Kingdom; 3 Medical Research Council Rosalind Franklin Centre for Genomics Research, Hinxton Genome Campus, United Kingdom

... Ab initio gene structures were predicted using FGENESH (Salamov and Solovyev 2000) and GENSCAN...


Current Proteomics,
January 2004, vol. 1, no. 1, pp. 41-48(8)

Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins

Authors: McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
Affiliations: 1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK.

... The polymorphic 'hypothetical transcriptome' was cons- tructed from transcripts predicted by FGENES, FGENESH ( Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...


Plant Physiology
, 2004

A Genome-Wide Screen Identifies Genes Required for Centromeric Cohesion

JJ Doyle, J Denarie, F Debelle, JC Prome, BB Amor, ...

... 17. HK Choi et al., Genetics, in press. 18. FGENESH, see www.softberry.com/berry.phtml. 19. E. Bornberg-Bauer, E. Rivals, M. Vingron, Nucleic Acids Res. ...


Proc Natl Acad Sci U S A.
2003 July 22; 100(15): 9055-9060.

Gene expression of a gene family in maize based on noncollinear haplotypes

Rentao Song and Joachim Messing*
Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020

.. The FGENESH program (Softberry, Mount Kisco, NY) was used for gene prediction analysis.


Fungal Genetics and Biology
Volume 39, Issue 1, June 2003, Pages 31-37

Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans

Alexander Idnurm and Barbara J. Howlett
School of Botany, The University of Melbourne, Vic. 3010, Australia

... A 6088 bp sequence was obtained (GenBank AF525231) and an open reading frame of 529 amino acids was predicted with FGENESH software (www.softberry.com) with no ...


The Journal of Experimental Biology
206, 1275-1289 (2003) doi: 10.1242/jeb.00261

Conservation of ecdysis-triggering hormone signalling in insects

Zitnan et al.,
1 Institute of Zoology, Slovak Academy of Sciences, Dubravska cesta 9, 84206 Bratislava, Slovakia 2 Institute of Medical Chemistry and Biochemistry, School of Medicine, Comenius University, Sasinkova 2, 81108 Bratislava, Slovakia

... The complete genomic sequence of the putative Anopheles eth gene was identified using the Softberry FGENESH gene prediction program (Salamov and Solovyev, 2000 ...


BMC Genomics.
2003; 4: 22.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

Sreedhar Oduru et al
1Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas. USA

... Two gene prediction programs were used FGENESH http://www.softberry.com/berry.phtml and GENEMARK http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi?org=H ...


Insect Molecular Biology
Volume 12 Issue 4 Page 319 - August 2003

Expression of an Aedes aegypti cation-chloride cotransporter and its Drosophila homologues

V. Filippov, K. Aimanova and S. S. Gill
Affiliations. Department of Cell Biology and Neuroscience, University of California, Riverside, USA

... significant similarity to the Drosophila genes were used for gene structure prediction with the FGENESH program available on site http:/ / www.softberry.com . ...


Developmental Biology
256 (2003) 276-289

tcl-2 encodes a novel protein that acts synergistically with Wnt signaling pathways in C. elegans

Xiaojun Zhao,a Hitoshi Sawa,b and Michael A. Hermana,*
a Program in Molecular, Cellular and Developmental Biology, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
b Laboratory for Cell Fate Decision, RIKEN, Center for Developmental Biology 2-2-3 Minatojima-minamimachi Chuo-ku, Kobe 650-0047, Japan

...CbTCL-2 is conceptually translated from a gene predicted by the FGENSH (Salamov and Solovyev, 2000; http://www.softberry.com) using defaults for C. elegans genomic sequences.


Proc Natl Acad Sci U S A.
2003 May 27; 100(11): 6569-6574.

Molecular paleontology of transposable elements in the Drosophila melanogaster genome

Vladimir V. Kapitonov* and Jerzy Jurka*
Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043

...We used FGENESH (ref. 18; www.softberry.com) for identifying genes encoded by TEs.


Genetics and Molecular Biology
ISSN 1415-4757 version impresa Genet. Mol. Biol. v.26 n.4 Sao Paulo dic. 2003

Iron homeostasis related genes in rice

Jeferson GrossI, II; Ricardo Jose SteinII; Arthur Germano Fett-NetoI, II; Janette Palma FettI, II
IUniversidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Porto Alegre, RS, Brazil

...The prediction algorithms were GenScan (Burge and Karlin, 1997; http://genes.mit.edu/GENSCAN.html), GenomeScan (Burge and Karlin, 1997; http://genes.mit.edu/genomescan.html), FGENESH (Salamov and Solovyev, 2000; http://www.softberry.com/berry.phtml?topic= gfind), GeneMark.hmm (Borodovsky and Lukashin, unpublished; http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi) and GrailEXP (Xu and Uberbacher, 1997; http://compbio.ornl.gov/grailexp/)...


BMC Plant Biology
2003, 3:6

Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)

Qian-Hao Zhu1,2, Mohammad Shamsul Hoque1,2, Elizabeth S Dennis1,2 and Narayana M Upadhyaya*1,2
Address: 1CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia and 2NSW Agricultural Genomics Centre, Wagga Wagga, Australia

... Analyses of 10-kb sequence of the ~30-kb contig 239 from the China Rice Genome database harboring the BFL1 locus by gene prediction programs FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN... ..The ORF was identified by using FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html.


Australasian Plant Pathology
Volume 32 Number 4 2003 pp. 511-519

Small scale functional genomics of the blackleg fungus, Leptosphaeria maculans: analysis of a 38 kb region

Alexander Idnurm, Janet L. Taylor, M. Soledade C. Pedras and Barbara J. Howlett

... vertebrate and Arabidopsis settings; Burge and Karlin 1997) and FGENESH on Neurospora crassa and Schizosaccharomyces pombe settings (www.softberry.com), as ...


Barley Genetics Newsletter
Volume 32 Hard-copy edition pages 34 - 37

MAPPING AND SEQUENCING OF THE BARLEY PUTATIVE HYPERSENSITIVE INDUCED REACTION GENES

Nils Rostoks1, David Kudrna1 and Andris Kleinhofs1,2
1 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
2 School of Molecular Biosciences, Washington State University, Pullman, WA 99164

The full length coding sequence was reconstructed using a combination of FGENESH gene prediction program (http://www.softberry.com/) and alignment with cDNAs from the other barley HIR groups.


TAG Theoretical and Applied Genetics
Issue: Volume 43, Number 5 Date: August 2003 Pages: 351 - 357

Characterisation of the mating-type locus of the plant pathogenic ascomycete Leptosphaeria maculans

Anton J. Cozijnsen A1 and Barbara J. Howlett A1
A1 School of Botany The University of Melbourne 3010 Victoria Australia

...Genes, introns, exons and transcription initiation sites were predicted by analysis with FGENESH (www.softberry.com) on Neurospora crassa and...


BMC Plant Biol.
2003; 3: 6.

Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)

Qian-Hao Zhu et al
1CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
2NSW Agricultural Genomics Centre, Wagga Wagga, Australia

...Analyses of 10-kb sequence of the ~30-kb contig 239 from the China Rice Genome database harboring the BFL1 locus by gene prediction programs FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html identified a single-exon gene capable of encoding a protein with the DNA binding domain of the EREBP/AP2 family of plant transcription factors [26,36], 1515 bp downstream from the Ds insertion. .. The ORF was identified by using FGENESH http://www.softberry.com/berry.phtml/ and GENSCAN http://genes.mit.edu/GENSCAN.html. Alignment of EREBP/AP2 domains was performed using programs of Genetics Computer Group Wisconsin software suit [11].


Genetics,
Vol. 164, 655-664, June 2003, Copyright © 2003

Map-Based Cloning of Leaf Rust Resistance Gene Lr21 From the Large and Polyploid Genome of Bread Wheat

Li Huang et al
a Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506-5502

...In addition, FGENSH 1.1 (http://www.softberry.com) was used for gene prediction (with monocot genomic DNA parameters).


Nucleic Acids Research,
2003, Vol. 31, No. 1 229-233

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists

Qiaoping Yuan et al
The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA

...The rice sequences were processed with multiple ab initio gene finders including FGENESH (http://www.softberry.com),... ... Working models were generated using the FGENESH output and putative identification for the gene was obtained from the most significant database match while models with no significant database match were labeled as hypothetical proteins.


Journal of Experimental Botany
, Vol. 54, No. 389, pp. 1995-1996, August 1, 2003

OsSET1, a novel SET-domain-containing gene from rice

Yun-Kuan Liang et al
PKU-Yale Joint Research Center of Agricultural and Plant Molecular Biology, National Key Laboratory of Protein Engineering and Plant Gene Engineering, College of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, PR China

... It localizes at chromosome three in rice genome at the contig 1300 (http://www.softberry.com/berry.phtml?topic=gfind&prg=FGENESH; GenBank accession number ...


BMC Genomics
2003, 4:22

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

Sreedhar Oduru et al
Address: 1Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas. USA

...Two gene prediction programs were used FGENESH http://www.softberry.com/berry.phtml and GENEMARK http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi?org=H.sapiens


TAG Theoretical and Applied Genetics
Issue: Volume 108, Number 5 Date: March 2004 Pages: 903 - 913

Characterization of soybean genomic features by analysis of its expressed sequence tags

Ai-Guo Tian et al
Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101 Beijing, China Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China

... prediction of these BAC-contig sequences was based on the gene-prediction program FGENSH (Arabidopsis match/FGENESH


Nucleic Acids Research
2002, Vol. 30, No. I 31-34

MIPS: a database for genomes and protein sequences

 Morgenstern, M Munsterkotter, S Rudd,  Weil

... mewes@gsf.de. ACKNOWLEDGEMENTS We thank V. Solovyev (Softberry Inc., NY) for providing and tuning the FGENSH program. This work was ...


Molecular Plant-Microbe Interactions
February 2002, Volume 15, Number 2 Pages 120-128 DOI: 10.1094/MPMI.2002.15.2.120

CPR1: A Gene Encoding a Putative Signal Peptidase That Functions in Pathogenicity of Colletotrichum graminicola to Maize

M. R. Thon, E. M. Nuckles, J. E. Takach, and L. J. Vaillanc
Department of Plant Pathology, S-305 Agricultural Sciences Center-North, University of Kentucky, Lexington 40546-0091, U.S.A.

... on-line from The Sanger Center's Computational Genomics Group); and a version of FGENESH trained on N. crassa sequences (available on-line from Softberry, Inc ...


Fungal Genetics and Biology
Volume 36, Issue 3, August 2002, Pages 234-241

Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus

Quere, Tomas Johansson and Anders Tunlid
Department of Microbial Ecology, Lund University, Ecology Building, S-223 62, Lund, Sweden

... gatech.edu/GeneMark/), the GlimmerM (www.tigr.org/softlab/glimmerm/), the ORF finder (www.ncbi.nlm.nih.gov/gorf/), and the FgeneSH (www.softberry.com/nucleo ...


Drug discovery today
Vol. 7, No. 11 (Suppl.), 2002, S70-S76 www.drugdiscoverytoday.com

Genome annotation techniques: new approaches and challenges

Alistair G. Rust Emmanuel Mongin and *Ewan Birney
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus Hinxton Cambridge UK CB10 1SD

... Examples of such prediction programs include Genscan [14] (used by Celera, ORNL and Ensembl), FGENESH [15] (used in the Softberry and UCSC browsers as well as ...
Box 1. Useful human genome annotation and browser URLs Human genome browsers
o UCSC Human Genome Browser: http://genome.cse.ucsc.edu/cgi-bin/hgGateway/
o Softberry Genome Explorer: http://www.softberry.com/berry.phtml?topic=genomexp
Ab initio gene prediction programs. Ab initio gene predictors rely on the statistical qualities of exons rather than on homologies. Examples of such prediction programs include Genscan [14] (used by Celera, ORNL and Ensembl), FGENESH [15] (used in the Softberry and UCSC browsers as well as Celera's pipeline) and GrailEXP [16] (ORNL).


Proc Natl Acad Sci U S A.
2002 August 20; 99(17): 11423-11428.

Identification of G protein-coupled receptors for Drosophila PRXamide peptides, CCAP, corazonin, and AKH supports a theory of ligand-receptor coevolution

Yoonseong Park,* Young-Joon Kim*, and Michael E. Adams*,
Departments of *Entomology and Cell Biology and Neuroscience, 5429 Boyce Hall, University of California, Riverside, CA 92521

...For each Drosophila GPCR, prediction of gene structure was made in FGENESH (www.softberry.com; ref. 21) by using about 20 kb of genomic sequence surrounding highly conserved regions, particularly for 5 prime and 3 prime ends of ORFs. Putative Drosophila GPCRs in the database were amplified by RT-PCR using primers based on gene predictions in the FGENESH gene finder (www.softberry.com; ref. 21). 21. Salamov A. A. & Solovyev, V. V. (2000) Genome Res. 10, 516-522....


Eukaryotic Cell,
October 2002, p. 719-724, Vol. 1, No. 5

Isocitrate Lyase Is Essential for Pathogenicity of the Fungus Leptosphaeria maculans to Canola (Brassica napus)

Alexander Idnurm and Barbara J. Howlett*
School of Botany, The University of Melbourne, Melbourne, Victoria 3010, Australia

... The DNA sequence obtained was compared to those in the GenBank database by using BLAST (1), and genes were predicted by using FGENESH software (http://www.softberry.com) and GENSCAN (www.bionavigator.com).


Biotech Software & Internet Report
November 2002, 3(5-6): 151-153. doi:10.1089/152791602321105834.

News

... sequence data. The genes are identified with the FGENESH11 gene modeling software exclusively li- censed from Softberry, Inc. Automatic ...


Genome
2002 Oct;45(5):963-72.
Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density ...

SA Brooks, L Huang, BS Gill, JP Fellers
Department of Plant Pathology, Kansas State University, Manhattan 66506, USA.

... trix. In addition, FGENESH 1.1 (http://www.softberry.com) was used for CDS prediction with monocot genomic DNA parameters. Both ...


Molecular Genetics and Genomics
Issue: Volume 267, Number 6 Date: August 2002 Pages: 713 - 720

Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion

Q. Yuan, J. Hill, J. Hsiao, K. Moffat, S. Ouyang, Z. Cheng, J. Jiang, C. Buell
A1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
A2 Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA

... The sequences were analyzed with several gene prediction programs, including FGENESH (http://www.softberry.com), Genemark.hmm (rice matrix; http://opal.biology ...


Genetics,
Vol. 162, 1389-1400, November 2002, Copyright © 2002

Different Types and Rates of Genome Evolution Detected by Comparative Sequence Analysis of Orthologous Segments From Four Cereal Genomes

Wusirika Ramakrishna et al
a Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907,

FGENESH (http://www.softberry.com/nucleo.html) with the maize training set was used for gene prediction in addition to GENSCAN (http://genes.mit.edu/GENSCAN.html) and GeneMark.hmm (http://genemark.biology.gatech.edu/Gene Mark/).


Nature
420, 316 - 320 (21 November 2002) | doi:10.1038/nature01183

Sequence and analysis of rice chromosome 4

Feng et al
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China Chinese National Human Genome Center at Shanghai, 351 Guo Shoujing Road, Shanghai 201203, China

FGENESH used for annotation of rice chromosome 4.


Functional & Integrative Genomics
Issue: Volume 2, Numbers 1-2 Date: May 2002 Pages: 51 - 59

Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley

Nils Rostoks et al
A1 Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA

... version 1.0 with maize parameters. The FGENESH predictions were run at http://www.softberry.com/. BAC genomic regions were defined ...


Genome
2003 Dec;46(6):1084-97
Structural organization of the barley D-hordein locus in comparison with its orthologous regions of wheat genomes
Gu et al.,
United States Department of Agriculture, Agriculture Research Service, Western Regional Research Center, Albany, CA 94710, USA

... et al. 1997) to search for additional genes. In addition, FGENESH (http://www.softberry.com/berry.phtml) and. GENESCAN (http://genes ...


PNAS
July 9, 2002 vol. 99 no. 14 9328-9333

The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases

R. Brueggeman et al
* Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420; Department of Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108-6030; and School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4234

.. The gene prediction programs GENSCAN (http://genes.mit.edu/GENSCAN.html) and FGENESH (http://www.softberry.com), as well as NEURAL NETWORK PROMOTER PREDICTION (http://www.fruitfly.org/seq_tools/promoter.html) localized the putative transcription start site of the gene about 400 bp upstream of the translation start site.


Plant Physiol.
2002 December; 130(4): 1626-1635.

Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize1

Rentao Song and Joachim Messing*
Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020

.. Draft sequences generated from high-throughput DNA sequencing (phase II) were subjected to gene prediction programs with FGENESH (Softberry, Inc., Mount Kisco, NY).


The Plant Cell,
Vol. 14, 3213-3223, December 2002,

Structural Analysis of the Maize Rp1 Complex Reveals Numerous Sites and Unexpected Mechanisms of Local Rearrangement

Wusirika Ramakrishnaa, John Embertona, Matthew Ogdena, Phillip SanMiguelb and Jeffrey L. Bennetzen1,a
a Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
b Purdue University Genomics Core, Purdue University, West Lafayette, Indiana 47907

... FGENESH (http://www.softberry.com/berry.phtml) with the monocot training set was used for gene prediction, in addition to GENSCAN (http://genes.mit.edu/GENSCAN ...


Plant Physiol.
2002 December; 130(4): 1728-1738.

Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex

Wusirika Ramakrishna, John Emberton, Phillip SanMiguel, Matthew Ogden, Victor Llaca, Joachim Messing, and Jeffrey L. Bennetzen
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 (W.R., J.E., M.O., J.L.B.); Purdue University Genomics Core, Purdue University, West Lafayette, Indiana 47907 (P.S.M.); and Waksman Institute, Rutgers University, Piscataway, New Jersey 08854 (V.L., J.M.)

...Annotation and sequence analysis were performed as described earlier (Dubcovsky et al., 2001 ; Song et al., 2001 ; Ramakrishna et al., 2002a ). FGENESH (http://www.softberry.com/berry.phtml) with the monocot training set was used for gene prediction in addition to GENSCAN (http://genes.mit.edu/GENSCAN.html) and GeneMark.hmm (http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi).


Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four ...

YQ Gu, D Coleman-Derr, X Kong, OD Anderson

... FGENESH (http://www.softberry.com/nucleo.html) and GENESCAN (http://genemark. mit.edu/GENESCAN.htm) were used for gene prediction. ...


Nature
419, 755 - 755 (17 Oct 2002) Technology Feature

Putting a name on it

Marina Chicurel

...used in the landmark publications of the draft human genome sequence. FGENESH, produced by software firm Softberry of Mount Kisco, New York, proved particularly useful for the Syngenta-led annotation of the rice genome sequence. Good...


FGENESH_GC

PLoS ONE
2012, 7(9): e44264. doi:10.1371/journal.pone.0044264

Identification and Sequence Analysis of Metazoan tRNA 3?-End Processing Enzymes tRNase Zs.

Wang et al.,
Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China

... The splicing pattern was verified using the Fgenesh and Fgenesh_GC programs provided at the Softberry website (http://linux1.softberry.com/berry.phtml??topic=fgenesh). ...


BMC Evolutionary Biology
2011, 11:219 doi:10.1186/1471-2148-11-219

A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2

Fan et al.,
1 Laboratory of Yeast Genetics and Molecular Biology, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China 2 Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China

...The splicing pattern was verified using the FGENESH and FGENESH_GC programs provided at the Softberry website...


Gene
Volume 451, Issues 1-2, 1 February 2010, Pages 6-14 doi:10.1016/j.gene.2009.08.018

Expression and regulation of IL-22 by bovine peripheral blood g/d T cells

Shi-Dong Ma, Cheryl A. Lancto, Shinichiro Enomoto, Mitchell S. Abrahamsen and Mark S. Rutherford
Department of Veterinary and Biomedical Sciences, University of Minnesota, 1988 Fitch Avenue, Room 295 AS/VM, St. Paul, MN 55108, USA

.. Genomic structure was deduced using FGENSH_GC program at http://www.softberry.com/berry. phtml?topic=fgeneshgc&group=programs&subgroup=gfind, and cDNA-genomic nucleotide sequences were aligned using Blast2 at http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2 ..


FGENES

Nucleosides, Nucleotides and Nucleic Acids
Volume 32, Issue 10, 2013 pages 529-554 DOI:10.1080/15257770.2013.832773

Gene Identification Programs in Bread Wheat: A Comparison Study

Nasiri et al.,
a Department of Agronomy and Plant Breeding, Division of Molecular Plant Genetics, College of Agricultural & Natural Resources , University of Tehran , Karaj , Tehran , Iran b Department of Plant Biotechnology, College of Agricultural & Natural Resources , University of Tehran , Karaj , Tehran , Iran

... Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10: 391–393. [CrossRef], [PubMed] View all references ] is an HMM-based variant of Fgenes that can be easily utilized online at softberry web server (http://linux1.softberry.com/berry.phtml). ...


Developmental & Comparative Immunology
Volume 34, Issue 2, February 2010, Pages 114-122 doi:10.1016/j.dci.2009.08.011

Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes

Francisco Gambon-Deza a, b, Christian Sanchez-Espinelb, 1, and Susana Magadan-Mompoc, 2,
a Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain b Shared Unity of Immunology, University of Vigo - Vigo University Hospital Complex (Hospital Meixoeiro), Edificio de Ciencias Experimentales, Rua das Abeleiras, Campus As Lagoas-Marcosende, Vigo 36310, Pontevedra, Spain

... immunoglobulin mRNAs. Limits of antibodies that were not yet published were deduced following the instructions in the software FGENES (www.softberry.com) and Augustus (http://augustus.gobics.de/submission). The results ... 


J Mol Diagn.
2010 Jul;12(4):520-4. Epub 2010 May 27

Comprehensive characterization of a novel intronic pseudo-exon inserted within an e14/a2 BCR-ABL rearrangement in a patient with chronic myeloid leukemia

Sorel et al.,
Service Service d'Hematologie et Oncologie Biologique - INSERM U935, Centre Hospitalier Universitaire de Poitiers, 2, rue de la Miletrie, 86021 Poitiers Cedex, France.

... Georgia Institute of Technology, Atlanta, GA; version 3.0; 2005; available at http://exon.gatech. edu/GeneMark/; accessed October 14, 2009), 6 and FGENES (SoftBerry, Mount Kisco, NY; 2007; available at http://linux1.softberry.com/berry.phtml; accessed October 14, 2009 ... 


Molecular Immunology
Volume 46, Issue 13, August 2009, Pages 2515-2523

The immunoglobulin heavy chain locus in the platypus (Ornithorhynchus anatinus)

F. Gambon-Deza, C. Sanchez-Espinel and S. Magadan-Mompo
aUnity of Inmunology, Vigo University Hospital Complex (CHUVI), Carretera de Madrid s/n., 36210 Vigo, Pontevedra, Spain bArea of Immunology, Faculty of Biology, University of Vigo, Department of Biochemistry, Genetics and Immunology, Rua das Abeleiras, Campus As Lagoas-Marcosende, 36310 Vigo, Pontevedra, Spain

... Limits of antibodies that were not yet published (IGHD and IGHY) were deduced following the instructions in the software FGENES (www.softberry.com) and Augustus (http://augustus.gobics. de/submission) together with the results obtained upon comparison with the reptilian ...


Developmental & Comparative Immunology
Volume 34, Issue 2, February 2010, Pages 114-122

Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes

F. Gambon-Deza, C. Sanchez-Espinel and S. Magadan-Mompo
a Unidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo 36210, Pontevedra, Spain

... immunoglobulin mRNAs. Limits of antibodies that were not yet published were deduced following the instructions in the software FGENES (www.softberry.com) and Augustus (http://augustus.gobics.de/submission). The results ...


Food and Chemical Toxicology
Volume 46, Issue 4, April 2008, Pages 1249-1256

SULT1C3, an orphan sequence of the human genome, encodes an enzyme activating various promutagens

Walter Meinl, Claudia Donath, Heiko Schneider Yasmin Sommer and Hansruedi Glat
German Institute of Human Nutrition (DIfE) Potsdam-Rehbru"cke, Department of Nutritional Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany

... SULT1 genes. No BLAST hit was observed for exon 4. It was found with the FGENES algorithm (hosted by http://www.softberry.com). Its ...


Acta Phytopathologica et Entomologica Hungarica
Volume 43, Number 1/June 2008 pp. 1-13

Cloning and characterization of a HOG-type MAP kinase encoding gene from Fusarium proliferatum

A. L. Adam, G. Kohut, L. Hornok
Szent Istvan University Agricultural Biotechnology Center, Mycology Group of the Hungarian Academy of Sciences, Institute of Plant Protection Pater K. u. 1 H-2103 Godollo Hungary

... Se- quence data were analyzed with the Lasergene (DNAStar Inc., USA) software package and the FGENES program (http://www.softberry.com). ...


Plant Pathology
Volume 57 Issue 5, Pages 861 - 869 Published Online: 21 Mar 2008

Peroxidases in the early responses of different potato cultivars to infection by Potato virus YNTN

M. Milavec, K. Gruden, M. Ravnikar, M. Kovac
National Institute of Biology, Vecna pot 111, 1000 Ljubljana, Slovenia

... Intron/exon structure of the gene was determined using FGENES 1·0, available online from SoftBerry (http://www.softberry.com/berry.phtml). ...


J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006

Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*

Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, and INSERM, U784, 75230 Paris, France

... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify potential first exons and/or splice donor sites. Signal ...


Cellular & Molecular Biology Letters
Volume 11, Number 2 / June, 2006 pp. 214-229

En/Spm-like transposons in Poaceae species: Transposase sequence variability and chromosomal distribution

Ahu Altinkut, Olga Raskina, Eviatar Nevo and Alexander Belyayev
Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, 31905, Israel

... The TPase open reading frame was assembled by removing introns using the FGENES 2.0 Program (http://www.softberry.com/berry.phtml?topic=fgenesh&group ...


Neuron
Volume 50 (2006), Issue 5, Pages 683-695

The Myotomal diwanka (lh3) Glycosyltransferase and Type XVIII Collagen Are Critical for Motor Growth Cone Migration

V. Schneider, M. Granato
University of Pennsylvania School of Medicine, Department of Cell and Developmental Biology, Philadelphia, Pennsylvania 19104

... Open reading frames within the diwanka interval were predicted with Genscan (http://genes.mit.edu/GENSCAN.html) and Fgenes (http://www.softberry.com/berry.phtml ...


Bioinformatics
2005 21(9):1776-1781; doi:10.1093/bioinformatics/bti283

Gene finding for the helical cytokines

Darrell Conklin 1,*, Betty Haldeman 2 and Zeren Gao 2
1Department of Computing, City University London, United Kingdom
2ZymoGenetics Inc. Seattle, USA

... For comparison purposes, three other gene finding methods were also run on the same dataset: Fgenes v1.6 (Solovyev et al., 1994), Genscan v1.0 (Burge and Karlin ...


Genes, Chromosomes and Cancer
Volume 43, Issue 1 , Pages 83 - 94 Published Online: 18 Feb 2005

Molecular cloning and characterization of FBXO47, a novel gene containing an F-box domain, located in the 17q12 band deleted in papillary renal cell carcinoma

Barbara Simon-Kayser et al
1Laboratoire d'Etude du Polymorphisme de l' ADN, Faculte de Medecine, Nantes, France

... html), GrailExp (http://grail.Isd.ornl.gov/grailexp), Fgenes (http://genomic.sanger. ac.uk/gf/gf.shtml), and Genmark (http://www2.ebi.ac.uk/genemark). ...


Journal of Neurobiology
Volume 63, Issue 3 , Pages 235 - 254 Published Online: 4 Mar 2005

Shaw potassium channel genes in Drosophila

James J. L. Hodge 1 2, James C. Choi 2, Cahir J. O'Kane 1 *, Leslie C. Griffith 2
1Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, United Kingdom
2Department of Biology and Volen Center for Complex Systems, Brandeis University MS008, 415 South Street, Waltham, Massachusetts 02454-9110

... Intron/exon structure of Shawl was initially predicted using the Fgenes program (Salamov and Solovyev, 2000) on the Baylor College of Medicine Genefinder ...


Current Proteomics,
January 2004, vol. 1, no. 1, pp. 41-48(8)

Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins

Authors: McGowan S.J.1; Terrett J.1; Brown C.G.1; Adam P.J.1; Aldridge L.1; Allen J.C.1; Amess B.1; Andrews K.A.1; Barnes M.1; Barnwell D.E.1
Affiliations: 1: Oxford GlycoSciences plc, The Forum, 86 Milton Park, Abingdon, OX14 4RY, UK.

... The polymorphic 'hypothetical transcriptome' was cons- tructed from transcripts predicted by Fgenes, FGENESH (Softberry Inc, Mount Kisco, NY, USA), GENSCAN ...


Nature Biotechnology
22, 1146 - 1149

5'-end SAGE for the analysis of transcriptional start sites

Hashimoto et al. (2004)..

...from expressed sequence tag (EST) maps, analysis of full-length cDNAs and computational annotation by Genscan, Genie, Fgenes and other programs.


Hemoglobin
Volume 28, Number 3 / 2004 255 - 259

An a-Thalassemia Phenotype in a Dutch Hindustani, Caused by a New Point Mutation that Creates an Alternative Splice Donor Site in the First Exon of the a2-Globin Gene

Cornelis L. Harteveld A1, Pierre W. Wijermans A2, Peter van Delft A1, Ellen Rasp A2, Hans L. Haak A2, Piero C. Giordano A1
A1 Hemoglobinopathies Laboratory, Leiden University Medical Center, PO Box 9503, 2300, Leiden, The Netherlands
A2 Leyenburg Hospital, The Hague, The Netherlands

... and GRAIL/ gap2 (Gene Recognition and Assembly Internet Link, Sequence exploration and gene discovery Version 1.3), Genefinder, GENSCAN, Fgenes and HMMGene ...


Journal of Medical Genetics
2004;41:e52

Genomic organisation of the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTAG) and its mutations in mucolipidosis III

A Raas-Rothschild et al
1 Department of Human Genetics, Hadassah University Medical Center, Jerusalem, Israel

... third intron is 9 kb. This structure was consistent with the exon prediction of fgenes and Genscan. Each splice donor and acceptor ...


Current Biology
2004, Volume 14, Issue 19, Pages R832-R833

Dual capacity of a human olfactory receptor

M. Spehr, K. Schwane, S. Heilmann, G. Gisselmann, T. Hummel, H. Hatt

... (B) RT-PCR with intron spanning primers. Candidates for 5'UTR exons were identified using FGENES and FEX software (SoftBerry, Mount Kisco, NY). ...


FGENES-M

Molecular Biology Reports
Volume 40, Issue 2 , pp 1201-1210 DOI: 10.1007/s11033-012-2162-2

Characterization of a vacuolar zinc transporter OZT1 in rice (Oryza sativa L.)

Lan et al.,
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

... genome database in GenBank with tblastn program. The identified homologous sequence was further analyzed for predicting the complete ORF with FGENES-M program (http://www.softberry.com). To verify the accuracy of gene ...


Molecular Biology Reports
Volume 36, Number 2 / February, 2009, pp. 281-287, DOI:10.1007/s11033-007-9177-0

Cloning and functional identification of two members of the ZIP (Zrt, Irt-like protein) gene family in rice (Oryza sativa L.)

Xia Yang 1, Ji Huang 1, Yan Jiang 1 and Hong-Sheng Zhang 1
(1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

... of China through tBLASTn algorithm program. The cDNA sequences of two putative rice ZIP genes with a complete ORF were assembled using FGENES-M program (http://www.softberry.com). Accord- ing to the predicted sequence ...


Molecular Biology Reports
Volume 35, Number 2 / June 2008 pp. 145-152

Molecular cloning and characterization of a novel SNAP25-type protein gene OsSNAP32 in rice ( Oryza sativa L.)

Yong-Mei Bao, Jian-Fei Wang, Ji Huang and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

... The genome organization and chromo- some mapping of the OsSNAP32 were investigated by the software FGENES-M at Softberry (http://www.softberry. ...


Molecular Genetics and Genomics
Volume 279, Number 3 / March, 2008 Pages 291-301

Cloning and characterization of three genes encoding Qb-SNARE proteins in rice

Yong-Mei Bao1, Jian-Fei Wang1, Ji Huang1 and Hong-Sheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

... The genome organization of three OsNPSNs were investigated using FGENES-M software (http://www.softberry.com/berry.phtml) by comparing the cloned cDNAs with ...


Gene
Volume 415, Issues 1-2, 31 May 2008, Pages 1-12

Expression analysis of the calcineurin B-like gene family in rice (Oryza sativa L.) under environmental stresses

Zhimin Gu et al.,
State key lab of crop genetics and germplasm enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China

... Fgenes-M (http://www.softberry.com), Genscan (http://genes.mit.edu/GENSCAN.html), BlastP (http://www.ncbi.nlm.nih.gov/BLAST/), National Centre for ...


Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
Volume 1769, Issue 4, April 2007, Pages 220-227

A novel rice C2H2-type zinc finger protein lacking DLN-box/EAR-motif plays a role in salt tolerance

Ji Huang1, a, Xia Yang1, a, Mei-Mei Wang2, a, Hai-Juan Tanga, Ling-Yun Dinga, Yin Shena and Hong-Sheng Zhang, a,
aState Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China

... probe sequence. The putative ORFs for these sequences were predicted with FGENES-M program (http://www.softberry.com). ZFP182, one ...


BMC Bioinformatics.
2005; 6: 25.

Integrating alternative splicing detection into gene prediction

Sylvain Foissac1 and Thomas Schiex1
1Unite de Biometrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan, France

..This approach has been applied eg. in HMMgene or in FGENES-M (unpub.)...


Molecular Biology Reports
Volume 32, Number 3 / September, 2005 pp.177-183

Rice ZFP15 Gene Encoding for a Novel C2H2-type Zinc Finger Protein Lacking DLN box, is Regulated by Spike Development but not by Abiotic Stresses

Ji Huang1, Jianfei Wang1 and Hongsheng Zhang1
(1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Rice Research Institute, Nanjing Agricultural University, Nanjing, 210095, China

... sequence. These sequences were analyzed with FGENES-M program (http://www. softberry.com) for predict- ing the complete ORFs. The ...


DNA Sequence - The Journal of Sequencing and Mapping
Volume 15, Number 1 / February 2004 39 - 43

Isolation and Characterization of Two cDNAs Encoding Translation Initiation Factor 1A from Rice(Oryza sativa L.)

Ji Huang, Jianfei Wang, Shengping Qiu, Hongsheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement Rice Research Institute Nanjing Agricultural University 210095 Nanjing People's Republic of China

... Then the ORF without introns was assembled based on the sequence of each scaffold using the program FGENES-M (http://www. softberry.com). ...


Plant Science
Volume 169, Issue 3, September 2005, Pages 470-477

Cloning and characterization of a novel rice gene family encoding putative dual-specificity protein kinases, involved in plant responses to abiotic and biotic stresses

Zhimin Gu, Jianfei Wang, Ji Huang and Hongsheng Zhang
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Department of Agronomy, Nanjing 210095, China

... genomic contigs having higher homology with the probe were obtained for prediction and assembling of putative ORFs by FGENES-M program (http://www.softberry.co


FGENESH-M

BMC plant biology
(2013). 13(1), 176. DOI:10.1186/1471-2229-13-176

An apple MYB transcription factor, MdMYB3, is involved in regulation of anthocyanin biosynthesis and flower development

Vimolmangkang, S., Han, Y., Wei, G., & Korban, S. S.
1 Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA 2 Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand

... Recovery of cDNA sequence encoding MdMYB3 in apple The genomic sequences encoding MdMYB3 were analyzed using FGENESH-M program (http://www. softberry. com), and an open reading frame (ORF) was predicted. ...


J. Exp. Bot.
(2012) 63 (1): 471-488. doi: 10.1093/jxb/err295

Two SERK genes are markers of pluripotency in Cyclamen persicum Mill.

Savona et al.,
1‘Sapienza’ University of Rome, Dept. of Environmental Biology, Rome, Italy 2‘Sapienza’ University of Rome, Dept. of Biology and Biotechnology, Rome, Italy

... programs (http://www.expasy.org/prosite/). ORFs were found with FGENESH-M (fgenesh-m; http://linux1.softberry.com/berry.phtml?topic=fgenesh-m&group= programs&subgroup=gfind). Phylogenetic analysis was performed by ...


Med. Chem. Commun.
2012,3, 987-996 DOI: 10.1039/C2MD20029E

Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(?)-notoamide, paraherquamide and malbrancheamide pathways

Shengying Li et al.,

... Phq protein). a Genes were predicted using the FGENESH-M tool from http://www.softberry.com; functions of gene products were predicted using BLAST search.b -: Homology cannot be calculated due to unrelatedness. NotA ...


J. Proteome Res.
2011, 10 (10), pp 4478–4504 DOI: 10.1021/pr200284e

Genomics, Transcriptomics, and Peptidomics of Daphnia pulex Neuropeptides and Protein Hormones

Dircksen et al.,
Department of Zoology, Stockholm University, Sweden Institute of Zoology, University of Cologne, Cologne, Germany Department of Biology, K.U. Leuven, Belgium

... More detailed analyses and novel annotations of genes, their exon-intron boundaries were performed usually with aid of Fgenesh-M gene finding tools (Softberry Inc., Mount Kisco, NY; http://linux1.softberry.com/berry.phtml?topic=fgenesh-m&group=programs&subgroup=gfind ...


Biochemical and Biophysical Research Communications
Volume 354, Issue 3, 16 March 2007, Pages 668-675

Sp-tetraKCNG: A novel cyclic nucleotide gated K+ channel

Blanca Estela Galindo, Jose Luis de la Vega-Beltran, Pedro Labarca, Victor D. Vacquier and Alberto Darszon
Depto. de Genetica del Desarrollo y Fisiologia Molecular del Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Apdo Postal 510-3, Cuernavaca, Morelos 62271, Mexico

... 3?-RACE was performed to obtain the 3?-end, and the 5?-end (684 nucleotides) was predicted by FGENESH-M, a program at the Softberry website (http://www ...


DNA Sequence - The Journal of Sequencing and Mapping
Volume 17, Number 1 / February 2006 pp. 24 - 30

Isolation and characterization of a new Na+/H+ antiporter gene OsNHA1 from rice (Oryza sativa L.)

Zhou et al.,
Nanjing Agricultural University, State key laboratory of crop genetics and germplasm enhancement, Nanjing, 210095, China

... An expected cDNA sequence containing a complete open reading frame (ORF) was predicted using FGENESH-M program (http://www.softberry. ...


BESTORF

BMC Genomics
2013, 14:695 doi:10.1186/1471-2164-14-695

Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles

Edwards et al.,
1 The Department of Microbiology, Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA 2 The Department of Microbial Infection and Immunity, Ohio State University, 484 W. 12th Ave., Columbus, OH 43210, USA

... Separately, the RNA-seq short reads were assembled into transcript contigs de novo (ie, independent of the reference genome sequence) using Inchworm [39] and open reading frames extracted from the transcripts with BestORF (Molquest package, Softberry). ...


PloS one
September 02, 2013DOI: 10.1371/journal.pone.0073560

Evolutionary History of Chordate PAX Genes: Dynamics of Change in a Complex Gene Family

Vanessa Rodrigues Paixao-Cortes, Francisco Mauro Salzano, Maria Catira Bortolini
Departamento de Genetica and Programa de Pos-Graduacao em Genetica e Biologia Molecular, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil

... The genomic sequences of possible unannotated orthologs were verified using three programs that can predict open reading frames (ORF): BESTORF (http://linux1.softberry.com/berry.phtml?? topic=bestorf&group=programs&subgroup=gf?ind), GeneWise (http://www.ebi.ac.uk ...


Nature Biotechnology
30, 549–554 (2012) doi:10.1038/nbt.2195

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Zhang et al.,
BGI-Shenzhen, Chinese Ministry of Agriculture, Key Lab of Genomics, Shenzhen, China.

... Open reading frames (ORFs) were predicted using BESTORF (http://linux1.softberry.com/berry.phtml?topic=bestorf&group=programs&subgroup=gfind) with parameters trained on monocot genes without filtering of UTRs. ...


Phytopathology
August 2012, Volume 102, Number 8 Pages 741-748 http://dx.doi.org/10.1094/PHYTO-02-12-0021-R

Role of the Pathotype-Specific ACRTS1 Gene Encoding a Hydroxylase Involved in the Biosynthesis of Host-Selective ACR-Toxin in the Rough Lemon Pathotype of Alternaria alternata

Izumi et al.,
Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795 Japan; Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430.

... Shimadze, Tsukuba, Japan). Putative open reading frames (ORFs) were identified using BESTORF (http://linux1.softberry. com/berry.phtml) from the sequence of the respective contigs by mass sequencing. Transcripts of ACRTS1 ...


Fungal Genetics and Biology
Volume 49, Issue 6, June 2012, Pages 470–482 DOI: 10.1016/j.fgb.2012.04.001

Transcriptome analysis of enriched Golovinomyces orontii haustoria by deep 454 pyrosequencing

We?ling et al.,
a Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Carl-von-Linne-Weg 10, 50829 Cologne, Germany b Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany

... Open reading frames were predicted from these contigs using BestORF with the Sclerotinia sclerotiorum matrix (Softberry, Mount Kisco, NY, USA). Predicted proteins were then annotated by Blast2Go (Conesa et al. 2005) using default parameters. ...


PLoS Pathog
8(4): e1002643. doi:10.1371/journal.ppat.1002643

Sequential Delivery of Host-Induced Virulence Effectors by Appressoria and Intracellular Hyphae of the Phytopathogen Colletotrichum higginsianum.

Kleemann et al.,
Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany Central Microscopy Max-Planck-Institute for Plant Breeding Research, Cologne, Germany

...ORFs were predicted from EST contigs with the Fusarium matrix of BESTORF (Molquest package, Softberry). ...


Nature
479, 529–533 (24 November 2011) doi:10.1038/nature10553

Ascaris suum draft genome

Jex et al.,
Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia BGI-Shenzhen, Shenzhen, 518083, China

...The open reading frame of each gene was predicted using BestORF (http://www.softberry.com). ...


PLoS ONE
2011, 6(2): e14697. doi:10.1371/journal.pone.0014697

ENCODE Tiling Array Analysis Identifies Differentially Expressed Annotated and Novel 5? Capped RNAs in Hepatitis C Infected Liver.

Folkers et al.,
Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America

...The use of a sequence analysis tool (BESTORF, www.softberry.com) to predict potential coding fragments in these unannotated sequences,...


MAKARA OF SCIENCE SERIES,
VOL 15, NO 2 (2011)

ISOLATION, CLONING AND CHARACTERIZATION OF ACTIN-ENCODING CDNAS FROM JATROPHA CURCAS L. IP-2P

Ratna Yuniati, Utut Widyastuti, Didy Sopandie, Akiho Yokota, Suharsono

... tool) (http://www.ncbi.nlm.nih. gov/BLAST/) program. The analysis of open reading frame (ORF) was carried out by using BESTORF program (http://www.softberry/bestorf/ htm). Phylogenetic analyses were conducted using MEGA ...


Appl. Comput. Math.
V.9, Special Issue, 2010, pp. 19-33

POSSIBLE FUNCTIONAL AND EVOLUTIONARY ROLE OF PLASTID DNA INSERTIONS IN RICE GENOME

YAGUT YU. AKBAROVA 1,2, VICTOR V. SOLOVYEV 3, ILHAM A. SHAHMURADOV 1
1 Bioinformatics Laboratory, Institute of Botany, Baku AZ1073, Azerbaijan 2 College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman 3 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20, UK

... of amino acid sequences has been carried out by BLAST program [1]. Search for statistically significant open reading frames (ORFs) and putative target compartments of proteins were done by BESTORF and ProtComp programs, respectively (http://www.softberry.com). ... 


BMC Genomics.
2010 Jul 8;11:422

Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)

Joly DL, Feau N, Tanguay P, Hamelin RC.
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P,O, Box 10380, Stn, Sainte-Foy, Quebec, QC, G1V 4C7, Canada.

... gene models. Initial ORF prediction for Melampsora spp. was generated with the bestORF algorithm (Softberry) using Ustilago parameters. Sequence analysis Similarity searches for full length sequences and conserved domains were performed ...


Molecular Vision
2009; 15:2544-2553

Phenotypic characterisation and ZEB1 mutational analysis in posterior polymorphous corneal dystrophy in a New Zealand population

Vincent et al.,
1Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand; 2Ophthalmology Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand

... Prediction of potential coding fragment in the reference mRNA (NM_0030751.4) sequence containing the c.1A?G was performed using the BESTORF program (Softberry.Inc, Mount Kisco, NY), and predicted translation initiation at nucleotide 788 which encodes the methionine ...


BMC Evolutionary Biology
2009, 9:97 doi:10.1186/1471-2148-9-97

Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa

Bert Breugelmans, Gert Simonet, Vincent van Hoef, Sofie Van Soest, Jozef, Vanden Broeck
Department of Animal Physiology and Neurobiology, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000 Leuven, Belgium

... presence of a signal peptide were predicted using BESTORF (http://www.softberry.com) and SignalP (http://www.cbs.dtu.dk/services/SignalP/), respectively. ... If no complete ORF was found, the Softberry splice finder tool (FSPLICE) was used to search the missing ...


FEBS Journal
Volume 275 Issue 6 Page 1103-1117, March 2008

Succinate dehydrogenase flavoprotein subunit expression in Saccharomyces cerevisiae– involvement of the mitochondrial FAD transporter, Flx1p

Teresa A. Giancaspero 1, Robin Wait 2, Eckhard Boles 3, Maria Barile
1 Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", Universita degli Studi di Bari, Italy 2 Kennedy Institute of Rheumatology Division, Faculty of Medicine, Imperial College London, UK 3 Institut fu"r Molekulare Biowissenschaften, J.W. Goethe-Universitat, Frankfurt am Main, Germany

... Both the NCBI tool orf finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and the bestorf gene prediction program from Softberry Inc. ...


Microbiology
154 (2008), 1204-1217; DOI 10.1099/mic.0.2007/014944-0

Identification of soluble secreted proteins from appressoria of Colletotrichum higginsianum by analysis of expressed sequence tags

Jochen Kleemann, Hiroyuki Takahara, Kurt Stu"ber and Richard O'Connell
Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Koln, Germany

... different reading frame. BESTORF (Softberry) was used to confirm the ORF of selected unique sequences. Proteins were considered ...


GENES & DEVELOPMENT
21:708-718, 2007

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay

Julie Z. Ni et al.,
Center for Molecular Biology of RNA and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA

... Once the transcripts are predicted, an ORF finder (BESTORF from Softberry, http://www.softberry.com) is used to find the best ORF. ...


Eukaryotic Cell, March 2005,
p. 526-535, Vol. 4, No. 3

Sex-Specific Homeodomain Proteins Sxi1 and Sxi2a Coordinately Regulate Sexual Development in Cryptococcus neoformans

Christina M. Hull,1, Marie-Josee Boily,1 and Joseph Heitman1,2*
Department of Molecular Genetics and Microbiology,1 the Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina2

... Sequence manipulations. Splice predictions of candidate gene sequences for SXI2a were facilitated with a Softberry algorithm (www.softberry.com). ...
...We utilized the BESTORF gene prediction algorithm from Softberry, Inc., to electronically produce predicted spliced cDNA products encoded by a 10-kb region....


SPL

Molecular and Cellular Endocrinology
Volume 348, Issue 1, 2 January 2012, Pages 313–321

Two novel mutations in the thyroglobulin gene as cause of congenital hypothyroidism: Identification a cryptic donor splice site in the exon 19

Hector M. Targovnik et al.,
a Laboratorio de Biologia Molecular, Catedra de Genetica y Biologia Molecular, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, 1113 Buenos Aires, Argentina b Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain c Service d’Endocrinologie Pediatrique, Hopital des Enfants, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse Cedex 9, France

... Searching for potential 5?ss sequences in the TG gene spanning exon 19 and intron 19 was accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.html), Fsplice (http://linux1.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind), SPL ...


Genome
2011, 54(12): 1041-1044, DOI: 10.1139/g11-068

Isolation of a strawberry gene fragment encoding an actin depolymerizing factor-like protein from genotypes resistant to Colletotrichum acutatum

Marta Ontivero, a Gustavo Martinez Zamor a,b Sergio Salazar, c Juan Carlos Diaz Ricci, b Atilio Pedro Castagnaro a
Seccion Biotecnologia, Estacion Experimental Agroindustrial Obispo Colombres-Unidad Asociada al INSIBIO, Av. William Cross 3150, 4101 Las Talitas, Tucuman, Argentina. bInstituto Superior de Investigaciones Biologicas (INSIBIO; CONICET- UNT) and Instituto de Quimica Biologica “Dr. Bernabe Bloj”, Universidad Nacional de Tucuman. Chacabuco 461, 4000 Tucuman. Argentina.

... The deduced amino acid sequence showed identity scores ranging between 93% and 60%, with E values comprised between 1 ? 10 –37 and 6 ? 10 –44 . The gene prediction programs SPL and FGENESH 2.6 (www.softberry.com) (Solovyev et al. ...


J Med Genet
2010 47: 8-21 originally published online July 1, 2009 doi: 10.1136/jmg.2009.067249

Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis)

Doherty et al.,
1University of Washington, Seattle, Washington, USA 2National Institutes of Health, Bethesda, Maryland, USA

... the likelihood that missense mutations would be deleterious was made using the PolyPhen program.42 NetGene2 (www.cbs.dtu.dk/services/NetGene2/), Genie (www.fruitfly.org/seq_tools/ splice.html), Human Splicing Finder (www.umd.be/HSF/), SPL (linux1.softberry.com), and ... 


Molecular breeding
2010, vol. 25, no4, pp. 699-722

Development of SSR markers and construction of a consensus genetic map for chicory (Cichorium intybus L.)

Cadalen et al.,
1) GIS CARTOCHIC, USTL, 59655, Villeneuve d’Ascq, France (2) UMR USTL/INRA 1281 «Stress Abiotiques et Differenciation des Vegetaux Cultives», ERT 1067, Universite de Lille 1, 59655, Villeneuve d’Ascq, France

... Intron positions were determined and then compared to predictions by models for intron/exon boundaries determination with RNA SPL tool, http://www.softberry.com/berry.phtml or GeneMark cDNA, http://opal.biology.gatech.edu/Gene Mark/genemark_cDNA_all.cgi. ... 


J Med Genet
doi:10.1136/jmg.2009.067249

Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis)

Doherty et al.,
University of Washington, United States

... likelihood that missense mutations would be deleterious was made using the PolyPhen program.[42] NetGene2 (www.cbs.dtu.dk/services/NetGene2/), Genie (www.fruitfly.org/seq_tools/ splice.html), Human Splicing Finder (www.umd.be/HSF/), SPL (linux1.softberry.com), and ...


European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21

Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda

Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China 2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China

...to search for cDNA and genomic DNA of SEDL-related splice variants.7 The FSPLICE 1.0 and SPL platforms (http://www.softberry.com/) were used to predict potential splice sites in genomic DNA. SPLM was implemented to substitute for SPL..


Blood Coagulation & Fibrinolysis.
19(3):240-242, April 2008.

Four novel FXI gene mutations in three factor XI- deficient patients

de Raucourt, Emmanuelle, de Mazancourt, Philippe, Quelin, Florence
Laboratory of Haematology, Poissy-Saint-Germain-en-Laye Hospital, France.

... exon 7, but an exon prediction software did not show an effect on the probability of splicing (website: http://www.softberry.com/cgi-bin/programs/gfind/spl.pl ...


Annals of Human Genetics
Volume 71 Issue 3 Page 325-335, May 2006

Common Polymorphisms in the CACNA1H Gene Associated with Childhood Absence Epilepsy in Chinese Han Population

J. Liang et al.,
Department of Pediatrics, Peking University, First Hospital, Beijing, 100034, P. R. China

... cmpharm.ucsf.edu/ ), transcription factor binding sites (NIH, http:/ / thr.cit.nih.gov/ molbio/ ), potential splicing sites (SPL, http:/ / softberry.com/ ...


J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006

Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*

Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, and ¶INSERM, U784, 75230 Paris, France

... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify potential first exons and/or splice donor sites. Signal ...


The National Academy of Sciences Proc Natl Acad Sci U S A.
2003 November 25; 100(Suppl 2): 14537-14542.

Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster

Hugh M. Robertson,* Coral G. Warr,and John R. Carlson

*Department of Entomology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801; School of Biological Sciences, Monash University, Clayton VIC 3800, Australia; and Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520

The genes were reconstructed manually in the PAUP editor (23) by using the expected exon/intron structures as guides and the SPL program (Softberry, www.softberry.com/berry.phtml) to locate predicted introns.


SPLM

Hum. Mol. Genet.
(2012) 21 (16): 3647-3654. doi: 10.1093/hmg/dds194

Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23)

Webb et al.,
1UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK, 2Jules Stein Eye Institute, University of California, 200 Stein Plaza, CA 90095-7000, USA

... SplicePredictor, http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi. FSplice, http://linux1.softberry. com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind. SPLM, http://linux1.softberry. com/berry.phtml?topic=splm&group=programs&subgroup=gfind. ...


European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21

Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda

Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China 2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China

... 7 The FSPLICE 1.0 and SPL platforms (http://www.softberry.com/) were used to predict potential splice sites in genomic DNA. SPLM was implemented to substitute ...


Fex

International Journal of Bioinformatics Research and Applications
Volume 9, Number 6/2013, pp. 557-575 DOI: 10.1504/IJBRA.2013.056630

In–silico analysis for RNA–interference mechanism of a–synuclein to treat Parkinson's disease

S. Seema 1, R. Seenivasagam 2, K. Hemavathi 3
1Department of Bioinformatics, University of East London, Docklands Campus, University Way, London E16 2RD, UK 2Division of Drug Discovery and Development, Center of Molecular and Computational Biology, Department of Botany, St. Joseph's College, P.B. 27094, 36, Langford Road, Bangalore, Karnataka 560027, India 3Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur - 613 402, Tamil Nadu, India

... 2009). The FEX program (Find EXon) (http://www.softberry.com/berry.phtml) predicts internal exons by linear discriminate function, evaluating ORFs flanked by GT and AG base pairs (the 5? and 3? ends of typical introns). ...


Plant Molecular Biology Reporter
April 2013, Volume 31, Issue 2, pp 303-313, DOI: 10.1007/s11105-012-0499-2

Molecular characterization of a cellulose synthase gene (AaxmCesA1) isolated from an Acacia auriculiformis x Acacia mangium hybrid

Seok Yien Christina Yong 1 and Ratnam Wickneswari 2
(1)Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia (2)School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia

... cgi /iprscan.cgi). Promoter sequence was analyzed using Prediction of Plant Promoter (http:// www.softberry.com/berry.phtml) and Neural Network Pre- diction (http://www.fruitly.org/seq_tools/promoter.html) software. The cDNA ... The software “Finding 5?, internal and 3? coding exons” (http://linux.softberry.com/cgi-bin/progrmas/gfind/fex.pl) was applied to predict exon–intron boundaries.


Cell Biology International.
(2013), doi: 10.1002/cbin.10080

Computational prediction and characterisation of ubiquitously expressed new splice variant of Prkaca gene in mouse.

Banday, A. R., Azim, S., Hussain, M. A., Nehar, S. and Tabish, M.
1Faculty of Life Sciences, Department of Biochemistry, A.M. University, Aligarh, Uttar Pradesh, India 2P.G. Department of Zoology, Ranchi University, Ranchi, Jharkhand, India

... (http://cbcb.umd.edu/software/GeneSplicer/) (Pertea et al., 2001), FGENESH (http://www.softberry. com/berry.phtml) and FEX (http://www.softberry.com/berry.phtml) and Augustus (http://augustus. gobics.de/) (Stanke et al., 2004). Alignment analysis was carried out using ...


Molecular Immunology
Volume 46, Issues 8-9, May 2009, Pages 1679-1687

The immunoglobulin heavy chain locus in the reptile Anolis carolinensis

Francisco Gambon Deza, Christian Sanchez Espinel and Susana Magadan Mompo
aUnidad de Inmunologia, Hospital do Meixoeiro, Carretera de Madrid s/n°, Vigo 36210, Pontevedra, Spain bInstituto Superior de Saude do Alto Ave (ISAVE), Quinta de Matos, Geraz do Minho, 4830-31 PVL, Portugal

... The constant region genes and exons were obtained by comparison with those already described for E. macularius. A dotplot was made with E. macularius and A. carolinensis sequences using the DNASTAR (lasergene), FGENESH and FEX software (http://www.softberry.com). ...


Fungal Genetics and Biology
Volume 44, Issue 5, May 2007, Pages 415-429

Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum

Ioannis Stergiopoulos et al.,
Laboratory of Phytopathology, Wageningen University and Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands

... Barcelona, Spain) and the FEX (Solovyev et al., 1994) and FGENESH (Salamov and Solovyev, 2000) programs from the MOLQUEST software package (Softberry Inc. ...


J. Biol. Chem.,
Vol. 281, Issue 40, 29753-29761, October 6, 2006

Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*

Juliette H. Faraco et al.,
Stanford University Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, and ¶INSERM, U784, 75230 Paris, France

... rate options. Fgenes, Fex, and Spl (Softberry.com) were used to identify potential first exons and/or splice donor sites. Signal ...


The Journal of Immunology,
2006, 176: 4221-4234.

Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region

Colette M. Johnston2, Andrew L. Wood, Daniel J. Bolland and Anne E. Corcoran3
Laboratory of Chromatin and Gene Expression, Babraham Institute, Babraham Research Campus, Cambridge CB2 4AT, United Kingdom

... and databases, thereby providing optimal consensus for gene predictions: GRAIL ( http://compblo.ornl.gov/Grail-1.3/ ), Fex ( http://www.softberry.com ), Hexon ...


Biochemical and Biophysical Research Communications
Volume 313, Issue 3, 16 January 2004, Pages 765-770

p73: in silico evidence for a putative third promoter region

A.Emre Sayana, Mario Rossia, Gerry Melinoa, b and Richard A Knight
Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK

... exons in these introns. Three out of six programs are the part of Softberry package [24] having different algorithms. FEX is looking ...


Current Biology
2004, Volume 14, Issue 19, Pages R832-R833

Dual capacity of a human olfactory receptor

M. Spehr, K. Schwane, S. Heilmann, G. Gisselmann, T. Hummel, H. Hatt

... (B) RT-PCR with intron spanning primers. Candidates for 5'UTR exons were identified using FGENES and FEX software (SoftBerry, Mount Kisco, NY). ...


RNASPL

BMC Genomics
2011, 12:110 doi:10.1186/1471-2164-12-110

Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1

Lu et al.,
The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Roslin, Midlothian, UK

... Pseudogenes were only annotated when their exons share at least 70% identity to the coding sequences. In addition, the exon-exon junctions of the predicted transcripts were predicted with the RNASPL program of the Softberry web server [61] to check for alternative splicing. ...


General and Comparative Endocrinology
Volume 169, Issue 3, 1 December 2010, Pages 192-196 doi:10.1016/j.ygcen.2010.09.014

Molecular cloning and characterization of preproorexin in winter skate (Leucoraja ocellata)

Erin E. MacDonald and Helene Volkoff
a Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada A1B 3X9 b Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada A1B 3X9

... Possible exon-exon locations were predicted using RNASPL (Softberry.com) and the most probable location was chosen based on the location of intron in known fish species (Faraco et al., 2006) and the fact that (A/C)AG is the most common exon sequence at the donor site ... 


FSPLICE

ISRN Computational Biology
Volume 2013 (2013), Article ID 790240, 6 pages http://dx.doi.org/10.1155/2013/790240

Zebra Finch Glucokinase Containing Two Homologous Halves Is an In Silico Chimera

Khrustalev Vladislav Victorovich, 1 Lelevich Sergey Vladimirovich, 2 and Barkovsky Eugene Victorovich 1
1Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, 220116 Minsk, Belarus 2Department of Clinical Laboratory Diagnostics, Allergology and Immunology, Grodno State Medical University, Gorkogo 80, 230009 Grodno, Belarus

... Levels of 1GC; 2GC and 3GC have been calculated by “VVK Protective Buffer” [5] in those newly described exons too. Splicing sites for “new” exons have been predicted by "FSPLICE" algorithm from SoftBerry server (http://linux1.softberry.com/). ...


BMC Genomics
2013, 14:34 doi:10.1186/1471-2164-14-34

Developmentally regulated expression and complex processing of barley pri-microRNAs

Kruszka et al.,
1 Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland 2 Computational Genomics Laboratory - Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland

...Intron positions were predicted by comparisons of genomic and cDNA sequences using FSPLICE software, http://linux1.softberry.com webcite[53]. ...


Hum. Mol. Genet.
(2012) 21 (16): 3647-3654. doi: 10.1093/hmg/dds194

Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23)

Webb et al.,
1UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK, 2Jules Stein Eye Institute, University of California, 200 Stein Plaza, CA 90095-7000, USA

... SplicePredictor, http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi. FSplice, http://linux1.softberry. com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind. SPLM, http://linux1.softberry. com/berry.phtml?topic=splm&group=programs&subgroup=gfind. ...


Journal of the Peripheral Nervous System
Volume 17, Issue 2, pages 141–146, June 2012 DOI: 10.1111/j.1529-8027.2012.00405.x

Two novel missense mutations in FGD4/FRABIN cause Charcot-Marie-Tooth type 4H (CMT4H)

Baudot et al.,
1Inserm, UMR 910, “Genetique Medicale et Genomique Fonctionnelle”, Faculte de Medecine de la Timone 2Aix-Marseille Univ, UMR 910, “Genetique Medicale et Genomique Fonctionnelle”, Faculte de Medecine de la Timone, Marseille, France

... variations on splicing was assessed using the following programs: ESE finder (http://rulai.cshl. edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home), NNSplice (http://biologyhelp.awardspace. com/desc.php?id=147&type=biotech), and FSPLICE (http://linux1.softberry.com/berry ...


Breast Cancer Research and Treatment
April 2012, Volume 132, Issue 3, pp 979-992 DOI 10.1007/s10549-011-1661-5

Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes

Mireia Menendez et al.,
1. Hereditary Cancer Program, Genetic Diagnosis Unit, Laboratori de Recerca Translacional, Institut Catala d’Oncologia, Hospital Duran i Reynals—Bellvitge Biomedical Research Institute (ICO-IDIBELL), L’Hospitalet de Llobregat, Barcelona and Hospital Josep Trueta, IDIBGI, Gran Via 199-203, Girona, 08908, Spain 2. Human Cancer Genetics, Spanish National Cancer Centre (CNIO), Madrid, Spain

... www.fruitfly.org/seq_tools/splice. html), NetGene2 Server (http://www.cbs.dtu.dk/ services/ NetGene2/) and SoftBerry (http://linux1.softberry.com/berry. phtml?topic= fsplice&group=programs&subgroup=gfind). In the case of intronic ...


Molecular and Cellular Endocrinology
Volume 348, Issue 1, 2 January 2012, Pages 313–321

Two novel mutations in the thyroglobulin gene as cause of congenital hypothyroidism: Identification a cryptic donor splice site in the exon 19

Hector M. Targovnik et al.,
a Laboratorio de Biologia Molecular, Catedra de Genetica y Biologia Molecular, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, 1113 Buenos Aires, Argentina b Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain c Service d’Endocrinologie Pediatrique, Hopital des Enfants, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse Cedex 9, France

... Searching for potential 5?ss sequences in the TG gene spanning exon 19 and intron 19 was accomplished using the NNSplice (http://www.fruitfly.org/seq_tools/splice.html), Fsplice (http://linux1.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind), SPL ...


Aging Cell
(2011), 10: 896–907. doi: 10.1111/j.1474-9726.2011.00727.x

Alternative splicing factor or splicing factor-2 plays a key role in intron retention of the endoglin gene during endothelial senescence.

Blanco, F. J. and Bernabeu, C.
Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), and Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), c/Ramiro de Maeztu 9, 28040 Madrid, Spain

... Genome Bioinformatics (http://genome.ucsc.edu/). Then, the FSPLICE and FGENESH tools were used to predict exons and introns in the DNA sequences (http://linux1. softberry.com/berry.phtml). The Transeq tool at the European ...


Clinical Gastroenterology and Hepatology
Volume 9, Issue 9 , Page 806, September 2011 DOI: 10.1016/j.cgh.2011.03.034

Lynch Syndrome in Young-Onset Colorectal Cancer: Reassessing the Role of the MSH6 Gene

Maria Dolores Giraldez, Antoni Castells, Sergi Castellvi-Bel
Department of Gastroenterology, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Spain

... By applying our strategy to the Limburg study (PolyPhen [http://genetics.bwh.harvard.edu/pph/], NNSPLICE [http://www.fruitfly.org/seq_tools/splice.html], and FSPLICE [http://linux1.softberry. com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind]), 8 of their patients ...

Phytopathologia Mediterranea
49, jan. 2011.

Amplification of Polyketide Synthase gene fragments in ochratoxigenic and nonochratoxigenic black aspergilli in grapevine.

STORARI, M., PERTOT, I., GESSLER, C., BROGGINI, G.

... Arbor, MI, USA). Putative introns were deter- mined using FSplice (www.softberry. com) and by homology with similar PKSs found in the NCBI database using BLASTX (http://blast.ncbi.nlm. nih.gov/Blast.cgi). Deduced amino ...



Chem. Senses
(2011) 36 (2): 149-160. doi: 10.1093/chemse/bjq105

Conservation of Indole Responsive Odorant Receptors in Mosquitoes Reveals an Ancient Olfactory Trait

Bohbot et al.,
1Departments of Biological Sciences and Pharmacology, Center for Molecular Neuroscience, Institutes of Chemical Biology and Global Health and Program in Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA 2Henry A. Wallace Beltsville Agricultural Research Center, Plant Sciences Institute, Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA

... Home.html). Matches were manually annotated using ClustalW and refined using the Softberry Splice Site Prediction program (http://linux1.softberry.com/berry.phtml? topic=fsplice&group=programs&subgroup=gfind). ClustalW ...


Microbiology
156 (2010), 2549-2557; DOI 10.1099/mic.0.039735-0

Molecular characterization and expression analysis of a suite of cytochrome P450 enzymes implicated in insect hydrocarbon degradation in the entomopathogenic fungus Beauveria bassiana

Nicolas Pedrini 1,2, Shizhu Zhang 1, M. Patricia Juarez 2 and Nemat O. Keyhani 1
1 Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA 2 Instituto de Investigaciones Bioquimicas de La Plata, CONICET, Facultad de Ciencias Medicas, UNLP, Calles 60 y 120 (1900), La Plata, Argentina

... Sequence analyses. The sequences were analysed using programs implemented at the Biology WorkBench website (http://workbench.sdsc.edu/); splice site analysis was performed using the FSPLICE program at the SoftBerry server (http://www.softberry.com/berry.phtml). ... 


Neurology
2010 Feb 2;74(5):366-71

Genetic contribution of FUS to frontotemporal lobar degeneration

Van Langenhove et al.,
Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerpen, Belgium.

.. the protein. The effect of sequence variants on splice site function and the prediction of alternative splice sites were assessed by the programs FSPLICE (http://www. softberry.com), NetGene2, 27 and NNSplice. 28. RESULTS. ... 


Chem. Senses
2010, doi: 10.1093/chemse/bjq105

Conservation of Indole Responsive Odorant Receptors in Mosquitoes Reveals an Ancient Olfactory Trait

Bohbot et al.,
1 Departments of Biological Sciences and Pharmacology, Center for Molecular Neuroscience, Institutes of Chemical Biology and Global Health and Program in Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA 2 Henry A. Wallace Beltsville Agricultural Research Center, Plant Sciences Institute, Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA

... Home.html). Matches were manually annotated using ClustalW and refined using the Softberry Splice Site Prediction program (http://linux1.softberry.com/berry.phtml? topic=fsplice&group=programs&subgroup=gfind). ClustalW ...


Neurology.
2010 Mar 9;74(10):846-50.

THAP1 mutations (DYT6) are an additional cause of early-onset dystonia

Houlden et al.,
From the Department of Molecular Neuroscience (H.H., R.P., A.M., J.H.), Sobell Department of Motor Neuroscience and Movement Disorders (S.A.S., P.S., M.E., K.P.B.), University College London Institute of Neurology, England;

... This intronic change is unlikely to be pathogenic because it did not affect splicing using the SpliceView program (http://bioinfo.itb.cnr.it/oriel/splice-view.html), NNSPLICE 0.9 (http://www.fruitfly.org/seq_tools/splice.html), and FSPLICE 1.0 (http://linux1.softberry.com/berry. ... 


Eur J Hum Genet.
2011 Jan;19(1):56-63. Epub 2010 Aug 18

Characterization of novel SLC6A8 variants with the use of splice-site analysis tools and implementation of a newly developed LOVD database

Betsalel et al.,
Metabolic Unit, Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands.

... Project 6 (http://www.fruitfly.org/seq_tools/splice.html), Netgene2 7 (http://www.cbs.dtu.dk/services/ NetGene2/), Splice Predictor 8 (http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi), GenscanW 9 (http://genes.mit.edu/GENSCAN.html) and FSplice (http://linux1.softberry.com/berry.phtml ... 


Hum. Mol. Genet.
2010 19 (21): 4201-4206. doi: 10.1093/hmg/ddq338

A novel SOD1 splice site mutation associated with familial ALS revealed by SOD activity analysis

Birve et al.,
1Department of Pharmacology and Clinical Neuroscience and 2Department of Medical Biosciences, Clinical Chemistry, Umea University, Umea, Sweden

... The analyses of mRNA (Fig. 1B), fibroblast extracts (Fig. 2A) and erythrocytes (Fig. 2B) combine to show that the usage of the alternative splice site must be close to complete for the mutant allele, which was only predicted by the program FSPLICE at www.softberry.com. ... 


BMC Evolutionary Biology
2009, 9:97 doi:10.1186/1471-2148-9-97

Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa

Bert Breugelmans, Gert Simonet, Vincent van Hoef, Sofie Van Soest, Jozef, Vanden Broeck
Department of Animal Physiology and Neurobiology, Zoological Institute, K.U.Leuven, Naamsestraat 59, B-3000 Leuven, Belgium

... presence of a signal peptide were predicted using BESTORF (http://www.softberry.com) and SignalP (http://www.cbs.dtu.dk/services/SignalP/), respectively. ... If no complete ORF was found, the Softberry splice finder tool (FSPLICE) was used to search the missing ...


PLoS ONE.
2009; 4(2): e4372.

Identification of Lympho-Epithelial Kazal-Type Inhibitor 2 in Human Skin as a Kallikrein-Related Peptidase 5-Specific Protease Inhibitor

Ulf Meyer-Hoffert, Zhihong Wu, and Jens-Michael Schroder
Department of Dermatology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany

... Subsequent sequence manipulations utilized the online BLAST 2 Sequences [37] (http://www.ncbi.nlm.nih.gov/ blast/bl2seq/bl2.html). Splice site analysis was performed using the FSPLICE program implemented at the SoftBerry server (http://www.softberry.com/berry.phtml). ...


Fungal Genetics and Biology
Volume 46, Issue 1, Supplement 1, March 2009, Pages S14-S18

Analysis and prediction of gene splice sites in four Aspergillus genomes

Kai Wang, David Wayne Ussery and Soren Brunak
aCenter for Biological Sequence Analysis, Department of Systems Biology, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark

... 1407 donor sites), and most of them are likely to be false positives (Table 3). On the other hand, FSPLICE predicts splice sites based on weight matrices model on many organisms including Aspergillus (www.softberry.com). ...


PLoS ONE.
2009; 4(4): e5227.

Molecular Identification and Expression Analysis of Filaggrin-2, a Member of the S100 Fused-Type Protein Family

Zhihong Wu, Britta Hansmann, Ulf Meyer-Hoffert, Regine Glaser, and Jens-Michael Schroder
Department of Dermatology, University Hospital of Schleswig-Holstein, Kiel, Germany

... Subsequent sequence manipulations utilized the online BLAST 2 Sequences [62] (http://www.ncbi.nlm.nih.gov/ blast/bl2seq/bl2.html). Splice site analysis was performed using the FSPLICE program implemented at the SoftBerry server (http://www.softberry.com/berry.phtml). ...


European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21

Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda

Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China 2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China

...to search for cDNA and genomic DNA of SEDL-related splice variants.7 The FSPLICE 1.0 and SPL platforms (http://www.softberry.com/) were used to predict potential splice sites in genomic DNA. SPLM was implemented to substitute for SPL..


Genetics
Vol. 176, 749-761, June 2007

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

Pavel Neumann, Huihuang Yan and Jiming Jiang
Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706

... Splice site analysis was performed using the FSPLICE program implemented at the SoftBerry server (http://www.softberry.com/berry.phtml). ...


Journal of Biochemistry and Molecular Biology
Vol. 40, No. 2, March 2007, pp. 172-179

PCR-mediated Recombination of the Amplification Products of the Hibiscus tiliaceus Cytosolic Glyceraldehyde-3-phosphate Dehydrogenase Gene

Linghui Wu, Tian Tang, Renchao Zhou and Suhua Shi*
State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China

...The boundaries of exons/introns in the obtained sequences were determined using FSPLICE (Softberry Inc.) combined with BLAST (blastn, tblastx and bl2seq) (Altschul et al., 1997; Tatusova and Madden, 1999). ...


The American Journal of Human Genetics
2005, Volume 76, Issue 5, Pages 729-749

Diversity and Function of Mutations in P450 Oxidoreductase in Patients with Antley-Bixler Syndrome and Disordered Steroidogenesis

Huang et al.,

... and "Frame 7" (table 4), disrupted the canonical splice-acceptor or -donor sites; the splice-site recognition programs FSPLICE (see the Softberry Web site ...


Genome Explorer

Nature
425, 209-215 (11 September 2003) | doi:10.1038/425209a

Bioinformatics: Programmed for success

Steve Buckingham

... Three-way synteny from Softberry. Fast searching is also a feature of Genome Explorer from Softberry in Mount Kisco, New York, which uses the FMAP algorithm. ... ...... Softberry, for example, offers a number of gene-prediction programs that can be accessed over the web, including FGENESH, which ... The fully automated FGENESH++C will automatically annotate any genome (other than human) to a standard claimed to be indistinguishable ...


SPLICEDB

International Journal of Evolutionary Biology
Volume 2013 (2013), Article ID 818954, 10 pages http://dx.doi.org/10.1155/2013/818954

Conservation/Mutation in the Splice Sites of Cytokine Receptor Genes of Mouse and Human

Rosa Calvello, Antonia Cianciulli, and Maria Antonietta Panaro
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy

... invertebrates, fungi, protozoa, and plants [25–30]. Comprehensive databases have also been generated, for example, http://www.softberry.com/spldb/SpliceDB.html [29–31], and [26]. Cumulatively, the above-quoted papers report ...


European Journal of Human Genetics
12 Nov 2008, doi: 10.1038/ejhg.2008.21

Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda

Feng Xiong et al.,
1 Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China 2 Bio-X Center, Shanghai Jiao Tong University, Shanghai, China

... 9 Exons 3, 4, 5 and 6 (containing the ... canonical and noncanonical mammalian splice sites (SpliceDB) was used ... and SPL platforms (http://www.softberry.com/) were ...


JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 12, Number 6, 2005 Pp. 894-906

Finding short DNA motifs using permuted markov models

X Zhao, H Huang, TP Speed

... The data are human donor sequences from SpliceDB[9], a recently developed database of known mammalian splice site sequences (http://www.softberry.com/spldb ...


Current Opinion in Structural Biology
2004, 14:273-282

The evolving roles of alternative splicing

Liana F Lareau1, Richard E Green1, Rajiv S Bhatnagar2,3 and Steven E Brenner1,2_
Departments of 1Molecular and Cell Biology, and 2Plant and Microbial Biology, University of California, Berkeley, California 94720, USA 3Department of Dermatology, University of California, San Francisco, California 94143, USA

... [79] SpliceDBhttp://www.softberry.com/berry.phtml?topic?SpliceDBDatabase and composition statistics for mammalian splice sites inferred from ESTs [80] ...


Yearbook of Medical Informatics.
Review Paper. 2004 121-136

Curated databases and their role in clinical bioinformatics

CC Englbrecht, M Han, MT Mader, A Osanger KFX Mayer
MIPS, Institute for Bioinformatics

...SpliceDB http://www.softberry.com/spldb/SpliceDB.html Canonical and non-canonical mammalian splice sites [122]
122.Burset M, Seledtsov IA, Solovyev VV. SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res 2001;29:255-9


Nucleic Acids Research,
2001, Vol. 29, No. 1 255-259

SpliceDB: database of canonical and non-canonical mammalian splice sites

M. Burset, I. A. Seledtsov1 and V. V. Solovyev*
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK and 1Softberry Inc., 108 Corporate Park Drive, Suite 120, White Plains, NY 10604, USA


FGENESH+

Fungal Genetics and Biology
2014, 62, 55-61. DOI:10.1016/j.fgb.2013.10.013

MAT gene idiomorphs suggest a heterothallic sexual cycle in a predominantly asexual and important pine pathogen

Bihon, W., Wingfield, M. J., Slippers, B., Duong, T. A., Wingfield, B. D.
a Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa b Crop Protection Division, Vegetable and Ornamental Plant Institute, Agricultural Research Council, Private Bag X293, Pretoria 0001, South Africa

... Workbench. Contigs with sequences having high similarity to the M. graminicola MAT1-2-1 sequence were analysed using FGENESH+(http://linux1.softberry.com) and AUGUSTUS (http://augustus.gobics.de) gene prediction programs. ...


Apidologie
2014, 1-15 DOI:10.1007/s13592-014-0292-3

Putative orthologues of genetically identified Drosophila melanogaster chitin producing and organising genes in Apis mellifera

Wang, Y., Odemer, R., Rosenkranz, P., Moussian, B.
1. Animal Genetics, Interfaculty Institute for Cell Biology, Eberhard-Karls University of Tubingen, Auf der Morgenstelle 8, 72076, Tubingen, Germany 2. Apicultural State Institute, University of Hohenheim, August-von-Hartmannstr. 13, 70599, Stuttgart, Germany

... To search for possible exons in the 5? region of GB46725 (coding for the putative grainyhead orthologue), the respective region was scanned manually and by using the software Fgenesh+ (www.?softberry.?com) and Genscan (genes.mit.edu/GENSCAN.html). ...


Plant Pathology
2014 Volume DOI: 10.1111/ppa.12184

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense.

Fraser-Smith S. et al.,
1 The University of Queensland, St. Lucia, Qld, Australia 2 Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, ACT 2617, Australia

... Gene structure was predicted using homology to the Fol-Six8 protein with the program fgenesh+ (Softberry.). ... The amino acid sequence of the Foc-Six8 homologues was predicted using the program fgenesh+ (Softberry) using homology to the Fol-Six8 protein (Fig. ...


Journal of virology
2014, JVI-00209 DOI:

Functional annotation of Cotesia congregata bracovirus: identification of the viral genes expressed in parasitized host immune tissues

Chevignon G. et al.,
1 Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, universite Francois-Rabelais, Tours, France. 2 Commissariat a l'Energie Atomique et aux energies alternatives, Genoscope (Centre National de Sequencage) Evry, France.

... Whenever overlapping 242 consensus sequences encompassed an entire CDS predicted by FGENESH+ 243 software detection (SoftBerry platform, http://linux1.softberry.com/all.html) on the 244 CcBV integrated genome (14), the corresponding gene was considered to 245 ...


Physiologia plantarum
, 150(1), 32-45. DOI: 10.1111/ppl.12064

Transcriptional regulation of the V?ATPase subunit c and V?PPase isoforms in Cucumis sativus under heavy metal stress

Kabala K. et al.,
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

... cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Physiologia Plantarum
Volume 150, Issue 1, pages 32–45, January 2014 DOI:10.1111/ppl.12064

Transcriptional regulation of the V-ATPase subunit c and V-PPase isoforms in Cucumis sativus under heavy metal stress

Katarzyna Kabala*, Malgorzata Janicka-Russak, Malgorzata Reda, Magdalena Migocka
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

.. cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Molecular Biology Reports
Volume 40, Issue 4 , pp 2809-2820 DOI:10.1007/s11033-012-2296-2

Isolation and characterization of a Laccase gene potentially involved in proanthocyanidin polymerization in oriental persimmon (Diospyros kaki Thunb.) fruit

Qianni Hu, Chun Luo, Qinglin Zhang, Zhengrong Luo
1. Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Shizishan, Wuhan, 430070, China

... Co., Ltd. Bioinformatics analyses. The similar protein-based gene prediction was performed on the DkLAC1 by the SoftBerry tool (http://linux1.softberry.com/berry.phtml? topic=fgenes_plus&group=programs&subgroup=gfs). The ...


Phil. Trans. R. Soc. B
19 September 2013 vol. 368 no. 1626 20130047 DOI:10.1098/rstb.2013.0047

Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses

Bezier et al.,
1Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Universite Francois Rabelais, Parc de Grandmont, 37200 Tours, France 2Commissariat a l'Energie Atomique, Genoscope (Centre National de Sequencage), 2 rue Gaston Cremieux, CP 5706, 91057 Evry Cedex, France

... For both Cotesia spp., gene predictions were performed using a combination of FGENESH and FGENESH+ software from the SoftBerry platform with the Apis mellifera training set (http://linux1.softberry.com/all.htm) and from the EMBL-EBI platform using Wise2 algorithms (http ...


G3
March 1, 2013 vol. 3 no. 3 465-480 DOI:10.1534/g3.112.004986

Unequal Recombination and Evolution of the Mating-Type (MAT) Loci in the Pathogenic Fungus Grosmannia clavigera and Relatives

Tsui et al.,
*Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4 †Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4

... The assembled sequences were submitted to FGENESH+ within Softberry (http://www.softberry. ru/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs) for gene prediction and to determine the location of the coding/non coding regions, and manually annotated with ...


Plant and Soil
Volume 364, Issue 1-2 , pp 245-260 DOI:10.1007/s11104-012-1345-x

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

M. Migocka, A. Warzybok, G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland

... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was determined using FGENESH or FGENESH+ programs available on softberry.com ...


Plant Pathology
DOI:10.1111/ppa.12184

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense

Fraser-Smith et al.,
1The University of Queensland, St. Lucia, Queensland, Australia 2Cooperative Research Centre for National Plant Biosecurity, Australia

... Gene structure was predicted using homology to the Fol-Six8 protein with the software program FGENESH+ (Softberry, Mount Kisco, NY, USA). Nucleotide and amino acid ... program FGENESH+ (Softberry, Mount Kisco, NY, USA) using homology to the Fol-Six8 protein. ...


The FASEB Journal
January 2013 vol. 27 no. 1 86-97 DOI:10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK; and §Department of Genetics, University of Cambridge, Cambridge, UK

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH+ (http://linux1.softberry.com/), Wise2 (http://www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/GENSCAN.html). Mosquito rearing and mating analysis. ...


Science China Life Sciences
Volume 56, Issue 7 , pp 628-637 DOI:10.1007/s11427-013-4505-1

Cloning and characterization of the gene cluster required for beauvericin biosynthesis in Fusarium proliferatum

Zhang et al.,
14505. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China 24505. University of Chinese Academy of Sciences, Beijing, 100049, China

... analysis. Gene products of the individual ORFs were deduced and analyzed using the programs AUGUSTUS [18,19] and FGENESH (http://linux1.softberry.com/berry. phtml?topic =fgenes_plus&group=programs&subgroup=gfs). ...


J Phylogen Evolution Biol
Volume 1 • Issue 1 • 1000107 DOI:10.4172/jpgeb.1000107

Ancient Origin of Chaperonin Gene Paralogs Involved in Ciliopathies

Krishanu Mukherjee 1 and Luciano Brocchieri 2*
1Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32610-3610, USA 2Department of Molecular Genetics and Microbiology and Genetics Institute, University of Florida, Gainesville, FL 32610-3610, USA

from the genome and the corresponding query protein was used to guide the prediction of the complete structure of the newly-identified gene, based on homology and on intron-exon junction signals, using the gene-prediction software FGENESH+ [39] at the Softberry web-site (linux1.softberry. com). Reverse


G3
January 1, 2013 vol. 3 no. 1 41-63 doi: 10.1534/g3.112.004044

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Manning et al.,
*Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 †Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4 ‡Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006

...Protein-encoding genes were annotated using a combination of manual curation, EST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com) and GENEID (http://genome.crg.es/software/geneid). ...


Fungal Biology
Volume 117, Issue 6, June 2013, Pages 411–421 DOI:10.1016/j.funbio.2013.04.005

Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum

Tuan A. Duong a, Z. Wilhelm de Beer b, Brenda D. Wingfield a, Michael J. Wingfield a
a Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa b Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa

... Plasmids from the positive clones were extracted and inserts were sequenced by primer walking (sequencing primers are available on request). Genes present in the inserts were predicted using FGENESH+ (Salamov and Solovyev 2000) (http://linux1.softberry.com). ...


Gene
Volume 519, Issue 1, 25 April 2013, Pages 18–25 DOI:10.1016/j.gene.2013.01.058

Genome-wide identification and divergent transcriptional expression of StAR-related lipid transfer (START) genes in teleosts

Teng et al.,
a Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China b Graduate University of the Chinese Academy of Sciences, Beijing 100049, China c Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China

... Gene predicted using FGENESH+ software (http://linux1.softberry.com/berry.phtml). ... a–?Distinct expression pattern of STARTs suggests divergent functions in development. FGENESH+ software (http://linux1.softberry.com/berry.phtml). ...


PloS one
February 01, 2013DOI: 10.1371/journal.pone.0055185

Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens

Liu et al.,
State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

... Gene Finding and Annotation. Gene models were predicted independently with a set of gene finders including Augustus [58], GeneMark-ES [59], GeneId [60] and SoftBerry eukaryotic gene finding suite (Fgenesh and Fgenesh+) [61]. ...


PLoS biology
(2013). 11(6), e1001585. DOI:10.1371/journal.pbio.1001585

Co-Expression of VAL-and TMT-Opsins Uncovers Ancient Photosensory Interneurons and Motorneurons in the Vertebrate Brain

Fischer et al.,
Max F. Perutz Laboratories, University of Vienna, Vienna, Austria, Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria

...Full-length coding sequences were predicted with FGENESH+ (softberry.com) using Takifugu rubripes TMT-Opsin as input protein sequence. ...


PLoS genetics
(2013). 9(1), e1003233. DOI:10.1371/journal.pgen.1003233

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Condon et al.,
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [103] and Genewise ....


PLoS Pathog
8(12): e1003037. doi:10.1371/journal.ppat.1003037

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Ohm et al.,
United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [87] and Genewise...


BMC Plant Biology
2012, 12:235 http://www.biomedcentral.com/1471-2229/12/235

Endo-(1,4)-b?-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes

Buchanan et al.,
1 Australian Research Council Centre of Excellence in Plant Cell Walls, and the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, South Australia 5064, Australia. 2 Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc, 7300 NW 62nd Avenue, Johnston, IA 50131-1004, USA

...and were extracted using the FGENESH + program (Softberry, Inc. 116 Radio Circle, Suite 400Mount Kisco, NY 10549, USA)....


Molecular Reproduction and Development
Volume 79, Issue 6, pages 380–391, June 2012 DOI: 10.1002/mrd.22040

An oocyte-preferential histone mRNA stem-loop-binding protein like is expressed in several mammalian species

Aurore Thelie et al.,
1INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France 2CNRS, UMR7247, Nouzilly, France

... We extracted the syntenic regions in mammals, and then applied several prediction gene methods, including FGENESH+ (http://linux1.softberry.com/berry.phtml), Genscan (Burge and Karlin, 1997), and Genewise (Birney et al., 2004). ...


MPMI
DOI: Vol. 25, No. 2, 2012, pp. 180–190. DOI: 10.1094/ MPMI -08-11-0212

A Highly Conserved Effector in Fusarium oxysporum Is Required for Full Virulence on Arabidopsis

Louise F. Thatcher, Donald M. Gardiner, Kemal Kazan, and John M. Manners
CSIRO Plant Industry, Queensland Bioscience Precinct, St. Lucia, Queensland, 4067, Australia

... gene structure was predicted using homology to F. oxysporum f. sp. lycopersici SIX proteins with FGENESH+ (Softberry, Mount Kisco, NY, U.S.A.), ...


Chemistry & Biology
Volume 19, Issue 12, 21 December 2012, Pages 1611–1619 DOI: 10.1016/j.chembiol.2012.10.010

Terpendole E, a Kinesin Eg5 Inhibitor, Is a Key Biosynthetic Intermediate of Indole-Diterpenes in the Producing Fungus Chaunopycnis alba

Takayuki Motoyama1, Toshiaki Hayashi1, Hiroshi Hirota1, Masashi Ueki1, Hiroyuki Osada1
1 Chemical Biology Core Facility, Chemical Biology Department, RIKEN Advanced Science Institute, Wako-shi, Saitama 351-0198, Japan

... Nucleotide and amino acid sequence data were analyzed by DNASIS-Mac software (Hitachi Software Engineering, Tokyo, Japan). Open reading frames were predicted by FGENESH and FGENESH + software (Softberry, Mount Kiscko, NY). Construction of Recombinant Strains. ...


Fungal Genetics and Biology
Volume 49, Issue 9, September 2012, Pages 708–716 DOI: 10.1016/j.fgb.2012.06.010,

Protein phosphatase Z modulates oxidative stress response in fungi

Leiter et al.,
a Department of Microbial Biotechnology and Cell Biology, Faculty of Science and Technology, University of Debrecen, Egyetem ter 1, H-4032 Debrecen, Hungary b Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, Cerdanyola del Valles 08193, Barcelona, Spain

.. 5 2.2. Sequence analysis of fungal PPZ phosphatases DNA sequences were analyzed with FGENESH and FGENESH+ (http://www.softberry.com/berry.phtml; exon-intron analysis), WEBGENE (http://www.itb.cnr.it/sun/webgene; gene structure analysis), pDRAW32 (http://www ...


New Phytologist
Volume 194, Issue 4, pages 1001–1013, June 2012 DOI: 10.1111/j.1469-8137.2012.04128.x

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Olson et al.,
1 Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsvag 26, 750 05 Uppsala, Sweden 2 US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

... based – FGENESH+, Genewise (Birney & Durbin, 2000) seeded by BLASTx (Altschul et al., 1990) alignments against GenBank's database of nonredundant proteins (NR: http://www.ncbi.nlm.nih. gov/BLAST/); and EST-based – EST_map (http://www.softberry.com/) seeded by ...


International Journal of Food Microbiology
Volume 157, Issue 2, 2 July 2012, Pages 202–209 DOI: 10.1016/j.ijfoodmicro.2012.05.008,

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

Jure Piskur et al.,
a Wine Research Centre, University of Nova Gorica, Slovenia b Department of Biology, Lund University, Sweden

... 2) homology-based — FGENESH+; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and 3) EST-based — EST_map (http://www.softberry.com/) seeded by ...


Fungal Genetics and Biology
Volume 49, Issue 3, March 2012, Pages 217–226 DOI: 10.1016/j.fgb.2012.01.007

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Mahajabeen Padamsee et al.,
a Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States b Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, United States

... 2) homology-based – FGENESH +; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and (3) EST-based – EST_map (http://www.softberry.com/) seeded by ...


African Journal of Biotechnology
Vol. 11 (1), pp. 88-98, 3 January, 2012, DOI: 10.5897/AJB11.3474

Identification and characterization of the Bcl-2-associated athanogene (BAG) protein family in rice

Rashid Mehmood Rana 1, 2, Shinan Dong 1, Zulfiqar Ali 3, Azeem Iqbal Khan 4 and Hong Sheng Zhang 1
1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. 2 Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University Rawalpindi, Pakistan.

... The resultant six members of BAG family in rice were processed for further study. Genomic and cDNA sequences of these proteins were retrieved from NCBI and gene structure was predicted by FGENESH+ (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2012) doi: 10.1093/jxb/ers245 First published online: September 20, 2012

Functional analysis of OsHSBP1 and OsHSBP2 revealed their involvement in the heat shock response in rice (Oryza sativa L.)

Rashid Mehmood Rana 1,2, Shinan Dong 1, Haijuan Tang 1, Fiaz Ahmad 1 and Hongsheng Zhang 1
1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China 2 Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University Rawalpindi, Pakistan

... by one. The HSBP domain was identified by Pfam (PF06825) to confirm the presence of these proteins in rice. Gene structure was predicted by FGENESH+ (http://linux1.softberry.com/berry.phtml). The chromosomal location ...


Immunogenetics
September 2012 DOI 10.1007/s00251-012-0643-z

Identification of natural killer cell receptor genes in the genome of the marsupial Tasmanian devil (Sarcophilus harrisii)

Lauren E. van der Kraan (1) Emily S. W. Wong (1) Nathan Lo (2) Beata Ujvari (1) Katherine Belov (1)
1. Faculty of Veterinary Science, University of Sydney, B19 RMC Gunn, Sydney, NSW, 2006, Australia 2. School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia

... incomplete, a different gene prediction software, Softberry FGENESH+ (http://linux1.softberry.com/all.htm), was used to re-predict the sequences, incorporating protein homology informa- tion (the BLAST best hit). Functional ...


Gene.
2012 Apr 15;497(2):249-55. Epub 2012 Jan 31.

A novel Acetyl-CoA synthetase short-chain subfamily member 1 (Acss1) gene indicates a dynamic history of paralogue retention and loss in vertebrates.

Castro LF et al.,
University of Porto, Portugal.

... Intron/exon predictions were made with FGENESH+ (http://linux1.softberry.com/berry.138 phtml). 2.2. Phylogenetic analysis. The ACSS1 amino acid sequences retrieved from the genome search were aligned using MAFFT with the L-INS-i method (Katoh and Toh, 2008). ...


Genet. Mol. Res.
11 (4): 3676-3687 (2012) DOI http://dx.doi.org/10.4238/2012.August.17.3

Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.)

R.M. Rana1,2, S. Dong1, Z. Ali3,4, J. Huang1 and H.S. Zhang1
1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China 2Department of Plant Breeding and Genetics, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan

... Genomic and cDNA sequences of these proteins were retrieved from NCBI, and gene structure was predicted by FGENESH+ (http://linux1.softberry.com/ berry.phtml). The chromosomal location of each ATG6 gene in rice was determined from the rice physical map constructed by the International Rice Genome Sequencing Project (IRGSP) (http://rgp.dna.affrc.go.jp). Subcellular localization of the OsATG6 family was predicted by WoLF PSORT (Horton et al., 2006) and ProtComp (http://linux1.softberry.com/berry.phtml). ...


Plant Physiology October
2011 vol. 157 no. 2 757-769 DOI: 10.1104/pp.111.181990

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

Guo et al.,
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany

... Gordon et al., 1998). Primer walking and PCR were used to fill or polish gaps and ambiguous regions. Annotation was performed using FGENESH and FGENESH+ (http://linux1.softberry.com/berry.phtml). Spidey (http://www.ncbi ...


Parasitology Research
Volume 108, Issue 3 , pp 611-620 DOI: 10.1007/s00436-010-2104-7

Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison

Mei-Yen Goh, Mei-Zhen Pan, Damer P. Blake, Kiew-Lian Wan, Beng-Kah Song
1. School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor DE, Malaysia 2. Parasitology, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK

... Structural annotation of the putative EmPIP5K gene Open reading frame identification was performed by submitting consensus contig sequence to the ab initio gene-prediction programs AUGUSTUS version 2.0.3 (Stanke et al. 2008), FGENESH+ (http://www.softberry. ...


The Journal of Biological Chemistry
March 25, 2011 286, 10419-10428. doi: 10.1074/jbc.M110.179853

Two Novel Classes of Enzymes Are Required for the Biosynthesis of Aurofusarin in Fusarium graminearum

Frandsen et al.,
From the ‡Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, DK-1870 Frederiksberg, the §Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby

... default settings (12). Ad hoc ab initio gene modeling was performed using FGENESH and FGENESH+ (SoftBerry). Motifs in unaligned sequences were identified using Meta-MEME version 4.1.1 and MAST (13, 14). Primer design ...


Peptides
Volume 34, Issue 1, March 2012, Pages 193–200

An evolutionary comparison of leucine-rich repeat containing G protein-coupled receptors reveals a novel LGR subtype

Matthias B. Van Hiel a, b, 1, , Hans Peter Vandersmissen a, 1, , Tom Van Loy a, , Jozef Vanden Broeck a
a Animal Physiology and Neurobiology, Zoological Institute of the Katholieke Universiteit Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium b Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Melbourne, Victoria 3010, Australia

... 39, 60]. Possible incorrectly in silico predicted sequences were manually checked at the genomic DNA level and, where possible, repredicted using softberry (http://linux1.softberry.com/berry.phtml) FGENESH+. Sequences were ...


PLoS ONE
6(8): e24111. doi:10.1371/journal.pone.0024111

Topological and Functional Characterization of an Insect Gustatory Receptor

Zhang et al.,
The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing, China CSIRO Food Futures Flagship, Canberra, Australian Capital Territory, Australia

...The genomic scaffold sequences containing candidate genes were predicted using FGENESH+ (http://www.softberry.com/berry.phtml), BGF...


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184–194 DOI: 10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

Tiago M. Martins a, b, , , Virgilio E. do Rosario b, Ana Domingos a, b
a Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E ? 1e-04 was adopted for the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with multiple exons was predicted using the FGENESH and FGENESH+ software (http://www.softberry.com). ...


J. Exp. Bot.
(2011) 62 (15): 5641-5658. doi: 10.1093/jxb/err249

Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a

Wang et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

... online). The genes were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) with FRI and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2011) 62 (10): 3359-3374. doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

... Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


Plant Physiology
February 2011 vol. 155 no. 2 1013-1022 DOI: 10.1104/pp.110.169870

Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations

Skot et al.,
Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3EB, United Kingdom (L.S., R.S., A.T., K.S., D.T., G.L., I.A.); Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A.)

... The identity of LpFT3 was confirmed by direct sequencing of the Hd3a.1f/3r-positive BACs with coding sequence and protein prediction generated using FGENESH+ (http://www.softberry.com/ berry.phtml) and by direct comparison with other monocot FT sequences obtained ...


PLoS Pathog
(2011), 7(7): e1002137. doi:10.1371/journal.ppat.1002137

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens.

Klosterman et al.,
USDA-ARS, Salinas, California, United States of America University of California, Davis, California, United States of America

...Protein-encoding genes were annotated using a combination of manually curated genes, in addition to EST BLAST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com), and ...


PLoS ONE
(2011) 6(8): e22046. doi:10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs.

Zhang et al.,
Department of Biology, University of Padua, Padova, Italy, Abteilung fur Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universitat zu Kiel, Kiel, Germany

...To ensure correct gene structures of all putative GPCR genes, we predicted gene structures using GENSCAN [97], [98] and predictions were repeated using GENOMESCAN [97], [98], GENEWISE [99] and FGENESH/FGENESH+ [31]. Intron-exon structures were determined with the aid of GENEWISE [99] and/or PROT_MAP module of the Softberry software suite (website: www.softberry.org). ...

Nature Biotechnology
29, 922–927 (2011) doi:10.1038/nbt.1976

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.

Berka et al.,
Novozymes, Inc., Davis, California, USA. US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.

... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly; cDNA-based EST_map (http://www.softberry.com/) seeded ...


Insect Molecular Biology
Special Issue: The Aphid Genome
Volume 19, Issue Supplement s2, pages 141–153, March 2010 DOI: 10.1111/j.1365-2583.2009.00975.x

Identification of ion channel genes in the Acyrthosiphon pisum genome

Dale et al.,
1 Syngenta, Jealotts Hill Research Centre, Bracknell, Berkshire, UK; 2 MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK;

... eugenes.org/aphid/), was also queried. Softberry protein-based gene predictions software FGENESH+ (http://linux1.softberry.com/berry.phtml) was used to refine gene sequence data. Previously identified members of the Glutamate ... 


Plant Physiology Preview
Published on November 29, 2010; 10.1104/pp.110.169870

Allelic variation in the Lolium perenne L. (perennial ryegrass ) FLOWERING LOCUS T (LpFT3) gene is associated with changes in flowering time across a range of populations

Skot et al.,
1 Aberystwyth University; 2 Aarhus University

... was confirmed by direct sequencing of the Hd3a.1f/3r positive BACs with coding sequence and protein prediction generated using FGENESH+ (http://www.softberry.com/berry.phtml) ... (http://linux1.softberry.com/berry.phtml). Predicted secondary structures for the proteins ...


J. Exp. Bot.
2010 doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1 Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2 Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

.. Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184-194 doi:10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

ATiago M. Martins a, b, Virgilio E. do Rosario b and Ana Domingos a, b
Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E 1e-04 was adopted for 93 the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with 94 multiple exons was predicted using the FGENESH and FGENESH+ software 95 (http://www.softberry.com). ... 


Developmental & Comparative Immunology
Volume 34, Issue 1, January 2010, Pages 1-13 doi:10.1016/j.dci.2009.08.002

Structure and expression pattern of teleost caspase recruitment domain (CARD) containing proteins that are potentially involved in NF-?B signalling

M.X. Chang a, W.Q. Chen a, b and P. Nie a
aState Key Laboratory of Freshwater Ecology and Biotechnology, and Laboratory of Fish Diseases, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, PR China bCollege of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China

... Manual annotation of the orthologous genes was also performed using FGENESH+ to predict structures based on homology with human genes: “fish” specific parameters were applied in this program (http://linux1.softberry.com/berry.phtml). 2.2. Fish and cell line. ... 


Cytokine & Growth Factor Reviews
Volume 20, Issue 2, Pages 115-124

Structural conservation of interferon gamma among vertebrates

R. Savan, S. Ravichandran, J. Collins, M. Sakai, H. Young

... Initially, DYRK2, MDM, RAP1B, NUP107, SLC35E3, CNTN1B, OPN1SW1, CALU harboring scaffolds or contigs were identified. These contigs were then searched for IFN-? gene using FGENESH+ software and curated manually (http://www.softberry.com/berry.phtml). ...


Mol Biol Evol.
2009 May;26(5):1143-53. Epub 2009 Feb 19.

Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family

Lucas-Lledo JI, Lynch M.
Department of Biology, Indiana University, Bloomington, Indiana, USA.

... The FGENESH+ gene predictor (http://linux1.softberry.com/berry.phtml) was occasionally used to improve the translation of some unannotated eukaryotic genes. Results from different searches were merged and aligned using ClustalX 1.83 (Thompson et al. ...


Mol Biol Evol.
2009 Jul;26(7):1557-69. Epub 2009 Apr 6.

The Fruitless gene in Nasonia displays complex sex-specific splicing and contains new zinc finger domains

Bertossa RC, van de Zande L, Beukeboom LW.
Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, The Netherlands.

... 1990 Go ). In cases in which no or partial sequences were annotated, missing domains were predicted using FGENESH+ at http://linux1.softberry.com/berry.phtml (Solovyev et al. 2006 Go ) using already known protein sequences as template. ...


Genetics.
2009 May;182(1):145-59. Epub 2009 Mar 16.

The multi-AT-hook chromosomal protein of Drosophila melanogaster, D1, is dispensable for viability

Weiler KS.
Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA

... was identified by tBLASTn of D. simulans genomic sequence using the D. melanogaster protein as a query (http://insects.eugenes.org/species/blast/). FGENESH+ (http://www.softberry.com) was used to predict the partial protein sequence. ...


Science.
2009 May 1;324(5927):626-31.

Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis

Schweitzer et al.,
1 North Carolina State University, Raleigh, NC 27695, USA. 2 North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA.

... two extinct organisms: Mammut americanum (MOR 605) and T. rex (MOR 1125) (see table S1 and SOM appendix) (6). The Anolis carolinensis amino acid sequence was inferred with the use of FGENESH+ (gene prediction on the basis of protein homology; www.softberry.com). ...


BMC Genomics
2009, 10:553 doi:10.1186/1471-2164-10-553

Annotation and expression of carboxylesterases in the silkworm, Bombyx mori

Quan-You Yu 1,2, Cheng Lu *2, Wen-Le Li 2, Zhong-Huai Xiang 2 and Ze Zhang *1,2
1The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China and 2The Key Sericultural Laboratory of the Agricultural Ministry of China, Southwest University, Chongqing, 400716, China

... weak sequence similarity to any query sequence and its flanking regions (1 kb or more long) were extracted. Putative COE genes within the extracted sequences were predicted using BGF software [55] and Fgenesh+ (http://www.softberry.com/). Phylogenetic analysis ...


Nature Biotechnology
26, 553 - 560 (2008)

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Diego Martinez et al.,
Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico 87545, USA. Novozymes, Inc., 1445 Drew Ave., Davis, California 95618, USA.

... an ab initio gene predictor, Fgenesh 37 , specifically trained for this genome, and two homology-based gene predictors, Fgenesh+ (http://www.softberry.com) and ...


Genes & Dev.
2008. 22: 2869-2885 10.1101/gad.1691208

LAB-1 antagonizes the Aurora B kinase in C. elegans

De Carvalho, C. E. et al.,
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; 2 Department of Molecular Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA

... Prediction of the coding sequence in the respective region in 1003.1 and conceptual translation were performed using FGENESH+ (http://www.softberry.com/berry ...


Nature
Volume 453 Number 7198 pp1064 - 1071 (19 Jun 2008), doi: 10.1038/nature06967

The amphioxus genome and the evolution of the chordate karyotype.

Bowler et al.
# Department of Energy Joint Genome Institute, Walnut Creek California 94598, USA
# Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

... A\Supplementary Note 3. Annotation of protein coding genes 3.1 Expressed sequence tag sequencing. cDNA libraries for amphioxus were prepared from gastrula and neurula stage embryos, and from larvae as described by 6, and a single library was created for Petromyzon marinus (sea lamprey). Approximately 32,000 expressed sequence tags (ESTs) were attempted from each library. (Supplementary Table S6). 3.2 Gene prediction, functional annotation and quality control. The JGI Annotation Pipeline was used for annotation of the amphioxus v1.0 assembly described here. The pipeline includes the following steps: (1) repeat masking, (2) mapping ESTs, full length cDNAs, and putative full length known genes, (3) gene structure prediction using several methods, (4) protein functional annotation using several methods, and (5) combining gene predictions into a non redundant representative set of gene models, which are subject to genome-scale analysis. The genomic sequence, predicted genes and annotations of amphioxus, together with available evidence, are available at the JGI Genome Portal (www.jgi.doe.gov/Amphioxus) and from GenBank under accession number ABEP01000000. Transposons were masked using RepeatMasker 7 tools and a custom library of manually curated repeats (see above Supplementary Note 2.4). 480,070 ESTs were clustered into 77,402 consensus sequences and both individual ESTs and consensus sequences were mapped onto genome assembly using BLAT4. Gene predictors used for annotation of amphioxus v1.0 included ab initio FGENESH 8, homology- based FGENESH+ 8, homology-based GENEWISE 9, and EST-based ESTEXT (Grigoriev, unpublished, available upon request). ...


PLoS ONE.
2008; 3(3): e1889.

Genome-Wide Detection of Serpentine Receptor-Like Proteins in Malaria Parasites

Luciana Madeira et al.,
1Departamento de Parasitologia, Instituto de Ciencias Biome'dicas, Universidade de Sa~o Paulo, Sa~o Paulo, Brasil 2Departamento de Bioqui'mica, Instituto de Qui'mica, Universidade de Sa~o Paulo, Sa~o Paulo, Brasil

... These sequences were submitted to a HMM plus similar protein-based gene prediction using the FGENESH+ program [22] (http://www.softberry.com), setting the ...


Nature
2008, 4doi:10.1038/nature07410

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Bowler et al.
1. CNRS UMR8186, Department of Biology, Ecole Normale Supe'rieure, 46 rue d'Ulm, 75005 Paris, France
2. Stazione Zoologica 'Anton Dohrn', Villa Comunale, I-80121 Naples, Italy

... Gene predictors used for these annotations included ab initio Fgenesh 12 trained on sets of known genes and reliable homology-based gene models from P. tricornutum and T.pseudonana, and homology-based Fgenesh+ 12 and Genewise 13 seeded by BLASTX alignments against sequences in the NCBI non-redundant protein set. ...


Nucleic Acids Research
(2007), doi:10.1093/nar/gkm768

ChromDB: The Chromatin Database

Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA

... In many cases, we have derived our own transcript models from genomic sequences using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...


BMC Genetics
2008, 9:78 doi:10.1186/1471-2156-9-78

Genomic Complexity of the Variable Region-Containing Chitin-Binding Proteins in Amphioxus

Dishaw et al.,
All Children’s Hospital,Department of Molecular Genetics,801SixthStreet South,St. Petersburg,FL 33701,USA

... html),FGENESH and FGENESH+ (http://linux1.softberry.com/all.htm) or genomescan[63,66] (http://genes.mit.edu/genomescan. html).Details ...


Fish & Shellfish Immunology
Volume 22, Issue 4, April 2007, Pages 351-362

Characterization of an interleukin-15 like (IL-15L) gene from zebrafish (Danio rerio)

I. Gunimaladevi, Ram Savan, Kenji Sato, Ryoji Yamaguchi and Masahiro Sakai
he United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima, Japan

... 15 gene sequences. The intron-exon structure was determined by FGENESH+ (http://www.softberry.com/berry.phtml). Gene-specific ...


Fungal Genetics and Biology
Volume 44, Issue 2, February 2007, Pages 77-87

Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium

Phil Kersten and Dan Cullen
Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA

... Predictions were based on ab initio methods Fgenesh (Salamov and Solovyev, 2000), homology-based methods, Fgenesh+ (www.softberry.com) and Genewise (Birney and ...


J. Biol. Chem.
Vol. 282, Issue 19, 13984-13993, May 11, 2007

Molecular and Functional Characterization of Inositol Trisphosphate Receptors during Early Zebrafish Development

Rachel Ashworth et al.,
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom

... sequences using the FGENESH+ program, a hidden-Markov model-based algorithm for finding genes with protein similarity, accessible at the Softberry web site. ...


PLoS Biol
(2007) 5(10): e275 doi:10.1371/journal.pbio.0050275

A Novel Snf2 Protein Maintains trans-Generational Regulatory States Established by Paramutation in Maize

Hale CJ, Stonaker JL, Gross SM, Hollick JB
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America

... for CHR156 was identified from BAC CH201-3L17 (GenBank accession AC194602), and gene model prediction was performed using FGENESH+ (Softberry, http: / /www ...


Journal of Molecular Evolution
2007 Volume 65, Number 2 pp. 137-153

Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution

Krishanu Mukherjee and Thomas R. Burglin
Department of Biosciences and Nutrition, Karolinska Institutet, and School of Life Sciences, Sodertorns Hogskola, Huddinge, Sweden

... carried out with the genomic sequence using the MIT GENSCAN server (http://genes.mit.edu/GENSCAN.html), as well as the FGENESH+ server at Softberry (http://www ...


Genetics
Vol. 176, 599-609, May 2007

The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare)

Sebastien Faure, Janet Higgins, Adrian Turner and David A. Laurie
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom

... New gene predictions were made using FGENESH+ and PROT_MAP (http://sun1.softberry. com) for FT-like genes showing incorrect alignment within the PEBP domain and ...


PNAS
| May 1, 2007 | vol. 104 | no. 18 | 7705-7710

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Brian Palenik et al.,
aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304;

... Gene prediction methods used for annotation of two Ostreococcus genomes included ab initio Fgenesh (40), homology-based Fgenesh+ (SoftBerry), Genewise (41 ...


Nature Biotechnology
25, 319 - 326 (2007) Published online: 4 March 2007 | doi:10.1038/nbt1290

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Thomas W Jeffries et al.,
US Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin 53705, USA.
Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, Wisconsin 53706, USA.

... Gene prediction methods used for analysis of the P. stipitis genome include ab initio Fgenesh 44 , homology-based Fgenesh+ (http://www.softberry.com/) and ...


Molecular Plant Pathology
Volume 8 Issue 1 Page 111-120, January 2007

Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana

LAURA CONDE-FERRAEZ et al.,
Centro de Investigacion Cientifica de Yucatan (CICY), Calle 43 no. 130, Chuburna de Hidalgo, C.P. 97200, Merida, Yucatan, Mexico

... Identification of open reading frames (ORFs) and gene predictions were performed using FGENESH and FGENESH+ software (Softberry™, http:/ / www.softberry.com ...


Insect Molecular Biology
15 (5), 541 - 549. doi:10.1111/j.1365-2583.2006.00674.x

Proteomic analyses of male contributions to honey bee sperm storage and mating

A. M. Collins, T. J. Caperna, V. Williams, W. M. Garrett, J. D. Evans
Bee Research Laboratory, ARS, USDA, Beltsville, MD, USA; *Growth Biology Laboratory, ARS, USDA, Beltsville, MD, USA; and Biotechnology and Germplasm Laboratory, ARS, USDA, Beltsville, MD, USA

... 2006) combined with a partially redundant database of ab initio proteins predicted by Genscan (Burge & Karlin, 1997) and FGENESH+ ( http:/ / www.softberry.com ...


J. Biol. Chem.,
Vol. 281, Issue 51, 39388-39395, December 22, 2006

A Toll Receptor and a Cytokine, Toll5A and Spz1C, Are Involved in Toll Antifungal Immune Signaling in the Mosquito Aedes aegypti*

Sang Woon Shin1, Guowu Bian1, and Alexander S. Raikhel2
From the Department of Entomology and the Institute for Integrative Genome Biology, University of California, Riverside, California 92521

... possible orthologues of Drosophila Toll and Toll-5. The open reading frames from these two loci were predicted using FGENESH+ (27) (sun1.softberry.com) by ...


Nature
434, 980-986 (21 April 2005)

The genome sequence of the rice blast fungus Magnaporthe grisea

Dean et al.,
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter EX4 4QG, UK

...Gene predictions were performed using FGENESH/FGENESH1 + trained on M. grisea sequences (SoftBerry) and GENEWISE (Sanger Center) and validated against 65 characterized M. grisea genes. Additional information and gene identification...


Genome Research
14:685-692, 2004

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno1 et al
1 Department of Computer Science, Stanford University, Stanford, California 94305, USA

... Fgenesh+ gene prediction is conducted on sequences with protein homology ...


Genome Research 13:313-322 2003
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.313703.

A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences

Trees-Juen Chuang,1 et al
1Bioinformatics Research Center, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;

...Numerous ab initio prediction programs have been used extensively in genome annotation, including FGENESH (Solovyev et al. 1995; Salamov and Solovyev 2000),
...Successful implementation of this method includes AAT (Huang et al. 1997), FGENESH+ and FGENESH++ (Salamov and Solovyev 2000),...
. Among these programs FGENESH+ (and FGENESH++), GenomeScan, GeneWise, and Procrustes are combined tools of sequence homology and ab initio annotation.


Annual Review of Genomics and Human Genetics Vol. 3: 293-310 (Volume publication date September 2002)

DATABASES AND TOOLS FOR BROWSING GENOMES

Ewan Birney,1 Michele Clamp,2 and Tim Hubbard2

1European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; e-mail: birney@ebi.ac.uk
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; michele@sanger.ac.uk th@sanger.ac.uk

... Another predicted gene track on the UCSC browser comes from Softberry ( http:/ / www.softberry.com ) and uses a program Fgenesh+, which is based on HMMs and ...


FGENESH++

Nature Genetics
45, 456–461 (2013) doi:10.1038/ng.2569

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

Peng et al.,
Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China. National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

... as used in genomic sequencing. Annotation of protein-coding genes. Protein-coding gene models were derived from evidence-based FgeneSH++(Softberry) pseudomolecules (Supplementary Fig. 7). To facilitate gene models ...


Nature Genetics
43, 913–918 (2011) doi:10.1038/ng.889

The genome of the extremophile crucifer Thellungiella parvula

Dassanayake et al.,
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. Office of Networked Information Technology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

...Random shotgun genomic libraries were constructed according to the manufacturer's recommendations for each of the two pyrosequencing platforms, GS FLX Titanium (454 Life Sciences) and Illumina GA2 (Illumina). Newbler (454-Roche), ABySS29 and minimus2 (ref. 30) were used as the main assembly programs to generate the draft genome, and FGENESH++ (SoftBerry), GENSCAN, BLAST (see URLs) and Blast2GO12 were used to predict and annotate gene models. ... ...FGENESH++ (SoftBerry) was used to predict protein coding ORFs in the T. parvula draft genome masked for repetitive sequences, with parameters optimized for dicot plants and protein sequences from the NCBI non-redundant (NR) database as reference....


Insect Molecular Biology
Volume 19, Issue Supplement s2, pages 5–12, March 2010

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome

Legeai et al.,
1 INRA UMR, Le Rheu cedex, France; 2 INRIA Centre Rennes – Bretagne Atlantique, GenOuest, Campus de Beaulieu, Rennes, France;

... Evidence-based prediction programs such as Augustus (Stanke et al., 2006), Fgenesh++ (unpubl., http://www.softberry.com) or the NCBI RefSeq pipeline are generally considered most reliable because they are better able to characterize untranslated regions (UTRs) and ... 


J. Proteome Res.
2010, 9 (2), pp 990–996 DOI: 10.1021/pr900885k

A Hybrid, de Novo Based, Genome-Wide Database Search Approach Applied to the Sea Urchin Neuropeptidome

Menschaert et al.,
Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B-9000 Ghent, Belgium

... The gene prediction program, Fgenesh++ (www.softberry.com), was applied to the genomic sequences corresponding to the newly identified peptides. The softberry gene finding software has a model trained for the sea urchin. ... 


Nature
2008, 452, 949 - 955.

The genome of the model beetle and pest Tribolium castaneum.

Richards et al.
1. Human Genome Sequencing Cente
2. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

... Work at the BCM-HGSC was funded by grants from the NHGRI and USDA. FgenesH and FgenesH++ analysis was donated by Softberry Inc. This research was additionally supported in part by the Intramural...


Genome Biology
2006, 7(Suppl 1):S10 doi:10.1186/gb-2006-7-s1-s10

Automatic annotation of eukaryotic genes, pseudogenes and promoters

Victor Solovyev, Peter Kosarev, Igor Seledsov and Denis Vorobyev
Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
Softberry Inc., Radio Circle, Mount Kisco, NY10549, USA

... The Fgenesh++ gene prediction pipeline can identify 91% of coding nucleotides with a specificity of 90%. ...


Am. J. Hum. Genet.,
76:652-662, 2005

Position Effects Due to Chromosome Breakpoints that Map 900 Kb Upstream and 1.3 Mb Downstream of SOX9 in Two Patients with Campomelic Dysplasia

Gopalrao V. N. Velagaleti,1,2,* et al,.
Departments of 1Pathology and 2Pediatrics, University of Texas Medical Branch, Galveston; Departments of 3Molecular and Human Genetics and 4Pediatrics, Baylor College of Medicine, and 5Texas Children's Hospital, Houston; and 6Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN

...In an effort to identify possible transcripts that may be responsible for the CD phenotype, we used several gene-prediction programs and identified seven hypothetical transcripts in the region that spans 100 kb in either direction from the breakpoint on chromosome 17 Ecgenes H17C12306.1 and H17C12308.1, SGP genes Chr17_1538.1 and Ch17_1539.1, Fgenesh++ gene C17001650, and Genscan genes NT_010641.44 and NT_010641.45....


Genome Research
15:566-576, 2005

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

Namshin Kim1,2, Seokmin Shin2 and Sanghyuk Lee1,3
1 Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea; 2 School of Chemistry, Seoul National University, Seoul 151-747, Korea

...the structure of full-length mRNA can be inferred by examining the flanking genomic region, especially with the aid of ab initio gene predicting programs such as Genscan (Burge and Karlin 1997 ) and Fgenesh++ (Salamov and Solovyev 2000 )...


Plant Physiology
139:1612-1624 (2005)

Structure and Architecture of the Maize Genome

Haberer et al.,
Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft fur Strahlenforschung Research Center for Environment and Health, D–85764 Neuherberg, Germany (G.H., H.G., K.F.X.M.); Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141 (S.Y., C.R., S.R., B.B., C.N.);

... Genes were detected by applying FGeneSH++ (Salamov and Solovyev, 2000 Go ;


Genome Research
14:685-692, 2004

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno1 et al.
1 Department of Computer Science, Stanford University, Stanford, California 94305, USA;

... we built a three-way synteny map based on chains of Fgenesh++-predicted (Solovyev 2002 ) exons, rather than whole genes. ...


Genome Research
14:539-548, 2004

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Gregory M. Cooper1 et al
1 Department of Genetics, Stanford University, Stanford, California 94305, USA;

....The gene annotations used to classify the constrained elements contain nearly 40,000 genes, including RefSeq genes and gene predictions; they are based on annotations for the human, mouse, and rat genomes made by Fgenesh++ software developed by Softberry Inc. (Solovyev 2002; http://www.softberry.com )....


Nucleic Acids Research,
2003, Vol. 31, No. 1 207-211

The PEDANT genome database

Dmitrij Frishman*,1 et al
1 Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstadter Landstra?e 1, 85764 Neueherberg, Germany

... The mouse database contains 20 chromosome contigs with 37 793 genes predicted using the Fgenesh++ software (www.softberry.com). ...


Genome Research
13:1765-1774, 2003

Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay

Shirin Khambata-Ford1,5 et al
1 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;

...Of 858 sequences, 9% of GFP+ low clones and 8% of GFP+ high clones aligned to the 2-kb segment upstream of the transcription start site of a predicted gene in at least two of four data sets of predicted genes from Genscan, Ensembl, Softberry (Fgenesh++), and Acembly (category B in Table 1).


Genome Research
13:313-322 ©2003
Received March 27, 2002; accepted in revised form December 3, 2002.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.313703.

A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences

Trees-Juen Chuang,1 et al
1Bioinformatics Research Center, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;

...Numerous ab initio prediction programs have been used extensively in genome annotation, including FGENESH (Solovyev et al. 1995; Salamov and Solovyev 2000),
...Successful implementation of this method includes AAT (Huang et al. 1997), FGENESH+and FGENESH++ (Salamov and Solovyev 2000),...
. Among these programs FGENESH+ (and FGENESH++), GenomeScan, GeneWise, and Procrustes are combined tools of sequence homology and ab initio annotation.


Archives of Biochemistry and Biophysics
Volume 409, Issue 2, 15 January 2003, Pages 287-297

Mitochondrial and nucleocytoplasmic isoforms of O-linked GlcNAc transferase encoded by a single mammalian gene

Hanover et al.,
Laboratory of Cell Biochemistry and Biology, NIDDK, National Institutes of Health, Building 8, Room 402, 8 Center Drive, MSC 0850, NIH, Bethesda, MD 20892-0850, USA

... Ensembl, Fgenesh ++, and the TSSW Promoter Prediction algorithms (http://www.softberry.com/berry.phtml) were initially employed. ...


Cell,
Vol. 110, 521-529, August 23, 2002, Copyright .2002 by Cell Press

HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots

Astrid R.W. Schroder,1 et al
1Infectious Disease Laboratory

...An integration target sequence was scored as a part of a transcrip-tion unit if it was (1) a member of the Refseq set of well-studied genes (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) or (2) if , it was predicted to be a transcription unit by the ENSEMBLE (http://www.ensembl.org) or Fgenesh++ (http://www.softberry.com/Help/fgeneshplus2.htm) programs and if that assignment was supported by mRNA or spliced EST sequence evidence.


Genome Res.
2002. 12: 1549-1555

Mosaic Organization of Orthologous Sequences in Grass Genomes

Rentao Song, Victor Llaca 1, and Joachim Messing 2
Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020, USA

... Gene prediction was based on both GeneScan (http://genes.mit.edu/Genscan.html) and FGENESH++ (http://www.softberry.com./berry.phtml?topic=gfind). ...


Reprint from
Daily Biotech Updates . . . www .genengnews.com

Vol. 22, No. 17 , October 1, 2002

DrugDiscovery
Tech Note:An Enhanced Human-Genome Database Transforming Raw Human Sequence Data Into Useful Information

Christine Schuller, Ph.D., and Andreas Fritz, Ph.D

The Softberry analysis results, for which Biomax has the exclusive world-wide commercial license, contain approximately 40,000 genes, which agrees well with predictions of the total number of human genes (according to the International Human Genome Sequencing Consortium, or IHGSC).
... For example, 50% of the genes in the Biomax Human Genome Database are not found in the Ensembl database. ..
These genes (identified by FGENESH++ and Biomax, and not found in Ensembl database) comprise the following: 6% of genes classified as known genes, 50% classified as having some similarity to known genes, and 90% of the genes not having similarity to known genes
For human genome applications, the FGENESH++ software was first used to map known human genes using sequences available from the Reference Sequence (RefSeq) Project at the Nation al Center for Biotechnology Information (NCBI; Bethesda, MD; www.ncbi.nlm. nih.gov/LocusLink/refseq.html).
REFERENCES
1. Salamov AA and Solovyev VV,Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 391-7 (2000).


FGENESH-C

The FASEB Journal
January 2013 vol. 27 no. 1 86-97 DOI:10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK; and §Department of Genetics, University of Cambridge, Cambridge, UK

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH+ (http://linux1.softberry.com/), Wise2 (http://www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/GENSCAN.html). Mosquito rearing and mating analysis. ...


Gene
Volume 528, Issue 2, 10 October 2013, Pages 267–276 DOI:10.1016/j.gene.2013.06.062

The metacaspase gene family of Vitis vinifera L.: Characterization and differential expression during ovule abortion in stenospermocarpic seedless grapes

Zhang et al.,
a College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China b Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi 712100, China

... Intron and exon organizations of metacaspases were analyzed by using FGENESH-C (http://linux1.softberry.com/berryphtml?topic=fgenes_c&group=programs&subgroup=gfs); to determine the locations of metacaspases on chromosomes, the metacaspases were further used ...


The FASEB Journal
Published online before print September 20, 2012 DOI: 10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK;

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH (http://linux1.softberry.com/), Wise2 (http:// www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/ GENSCAN.html). Mosquito rearing and mating analysis ...


J. Exp. Bot.
(2011) 62 (15): 5641-5658. doi: 10.1093/jxb/err249

Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a

Wang et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

... online). The genes were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) with FRI and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2011) 62 (10): 3359-3374. doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

... Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


J. Exp. Bot.
2010 doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1 Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2 Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

.. Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


FGENESH-2

PLoS ONE
(2013), 8(1): e53525. doi:10.1371/journal.pone.0053525

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum s.s.

Dalman et al.,
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden

...he gene annotations found in TC32-1 were transferred to the reference sequence using PROT_MAP, FGENESH-2 (SoftBerry, Mount Kisco, NY) and Artemis ...


Eukaryotic Cell
August 2010, p. 1225-1235, Vol. 9, No. 8 doi:10.1128/EC.00031-10

Methylenetetrahydrofolate Reductase Activity Is Involved in the Plasma Membrane Redox System Required for Pigment Biosynthesis in Filamentous Fungi

Frandsen et al.,
Division

... MTHFR homologs in complete Ascomycota genomes were identified in the listed databases using the blastp and tblastn algorithms with default settings (1). All Pezizomycotina tblastn hits were annotated using FGENEH-2 from Softberry (Mount Kisco, NJ) with FgMET13p as a ... 


J Immunol.
2010 Feb 1;184(3):1379-91. Epub 2009 Dec 21

A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons

Abi-Rached et al.,
Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.

... Foster City, CA). Exons and introns of genes were either identified manually or by using the BLAST (www.ncbi.nlm.nih.gov/BLAST) and FGENESH-2 (www.softberry. com/all.htm) algorithms. Phylogenetic analysis of KIR. KIR gene ... 


The Journal of Immunology
2009, doi:10.4049/jimmunol.0903016

A Small, Variable, and Irregular Killer Cell Ig-Like Receptor Locus Accompanies the Absence of MHC-C and MHC-G in Gibbons

Abi-Rached et al.,
Department of Structural Biology, Stanford University, Stanford, CA 94305; Max Planck Institute for Molecular Genetics, Berlin-Dahlem

... Biosystems, Foster City, CA). Exons and introns of genes were either identified manually or by using the BLAST (www.ncbi.nlm.nih.gov/ BLAST) and FGENESH-2 (www.softberry.com/all.htm) algorithms. Phylogenetic analysis of KIR ...


PLoS Genet.
2009 Oct;5(10):e1000688. Epub 2009 Oct 16.

A novel system of polymorphic and diverse NK cell receptors in primates

Averdam et al.,
Department of Primate Genetics, German Primate Centre, Gottingen, Germany.

... Both programs are available from Phil Green, University of Washington. Exons and introns of genes were identified in finished BAC clone sequences manually or by BLAST and FGENESH-2 algorithms (http://www.ncbi.nlm.nih.gov/BLAST/; http://www.softberry.com/all.htm). ...


The Journal of Immunology
2007, 178: 7151-7161.

Genomics and Diversity of the Common Marmoset Monkey NK Complex

Anne Averdam et al.,
Department of Primate Genetics and Primate Husbandry, German Primate Center, Gottingen, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208

... BLAST and FGENESH-2 algorithms (http://www.ncbi.nlm.nih.gov/BLAST/; http://www.softberry.com/all.htm) identified exons and introns of genes in finished BAC ...


FGENESH++C

Nucleic Acids Research,
2006, Vol. 34, Database issue D568-D571

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context

Andreas Ruepp1,* et al.,
1Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany

... The basis of the MfunGD dataset is a complement of gene products that was obtained by Softberry Inc., which used the FGENESH++C software as gene predictor. ...


Nature
425, 209-215 (11 September 2003) | doi:10.1038/425209a

Bioinformatics: Programmed for success

Steve Buckingham

... Three-way synteny from Softberry. Fast searching is also a feature of Genome Explorer from Softberry in Mount Kisco, New York, which uses the FMAP algorithm. ... ...... Softberry, for example, offers a number of gene-prediction programs that can be accessed over the web, including FGENESH, which ... The fully automated FGENESH++C will automatically annotate any genome (other than human) to a standard claimed to be indistinguishable ...


FGENESB class="norm"> Frontiers in microbiology
2014, 5: 189. DOI: 10.3389/fmicb.2014.00189

Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome.

Culligan, E. P., Marchesi, J. R., Hill, C., & Sleator, R. D.
1Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland 2School of Microbiology, University College Cork, Cork, Ireland 3Cardiff School of Biosciences, Cardiff University, Cardiff, UK

... The retrieved sequence was analyzed using the FGENESB software program (Softberry) to identify putative open reading frames and translated nucleotide sequences were subjected to BLASTP analysis to assign putative functions to the encoded proteins and identify ...


Genome announcements
2014, 2(2), e00194-14. DOI: 10.1128/genomeA.00194-14

Draft genome sequence of Trueperella pyogenes, isolated from the infected uterus of a postpartum cow with metritis

Goldstone R. J. et al.,
aInstitute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom bInstitute of Life Science, School of Medicine, Swansea University, Singleton Park, Swansea, United Kingdom

... The prediction of open reading frames (ORFs) was achieved using FgenesB (8) via the SoftBerry web interface (http://linux1.softberry.com/berry.phtml), rRNA prediction was carried out via the HMMER Web server (9), and tRNA prediction was done using tRNAscan-SE via the ...


BioMed Research International
2014, Article ID 489782, 7 pages DOI: 10.1155/2014/489782

Characterization of the Opp Peptide Transporter of Corynebacterium pseudotuberculosis and Its Role in Virulence and Pathogenicity

Moraes P. M. R. O. et al.,
1Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil 2Instituto de Ciencias da Saude, Universidade Federal da Bahia, 40210-340 Salvador, BA, Brazil

... bacteria was performed using the Artemis software. The operon analyses were performed using SoftBerry (http://linux1.softberry.com/berry.phtml?topic= fgenesb&group=help&subgroup=gfindb). A similarity analysis of the genes ...


PloS one
2014, 9(2), e90087. DOI: 10.1371/journal.pone.0090087

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

Sierra-Garcia I. N. et al.,
Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil Laboratory of Genomics and Expression, University of Campinas - UNICAMP, Campinas, Brazil

... several tools available for gene prediction in prokaryotes through heuristic approaches: Metagene [14] http://metagene.cb.ku-tokyo.ac.jp/) and MetaGeneMark [15] designed for metagenomic sequences, GLIMMER 3.02 [16], [17] and FGENESB (http://linux1.softberry.com/berry ... ...Putative ribosomal binding sites were identified using RBSFINDER [22], and the presence of bacterial promoters and transfer RNA genes was predicted using the programs BPROM (http://linux1.softberry.com/berry.phtml) and tRNAscan-SE [23], respectively. ...


Plasmid
2014, 71, 23-31. DOI: 10.1016/j.plasmid.2013.10.002

Characterization of two novel plasmids from Geobacillus sp. 610 and 1121 strains

Kananaviciute, R., Butaite, E., Citavicius, D.
Department of Microbiology and Biotechnology, Faculty of Natural Sciences, Vilnius University, M. K. Ciurlionio 21/27, Vilnius LT-03101, Lithuania

... sequencing of remaining fragments. Open reading frames (ORFs) were predicted using ORF Finder Program at NCBI website and FGENESB program at Softberry site (http://linux1.softberry.com/berry.phtml). Potential protein-coding ...


Applied microbiology and biotechnology
2014, 98(5), 2145-2154. DOI: 10.1007/s00253-013-5126-0

Molecular cloning and characterization of a novel acetylalginate esterase gene in alg operon from Sphingomonas sp. MJ-3

Park Y. J. et al.,
1. Department of Food Science and Biotechnology, Kyungsung University, Busan, 608-736, Korea 2. College of Pharmacy, Kyungsung University, Busan, 608-736, Korea

... The PCR primers used for screening and sequencing are listed in Table 1. The positive fosmid DNAs were sequenced, and then genes or operon were ana- lyzed by using fgenesb program (http://linux1.softberry.com/ berry.phtml) and ORF finder (http://www.ncbi.nlm.nih.gov ...


Genome announcements
2014, 2(2), e00243-14. DOI: 10.1128/genomeA.00243-14

Genome sequence of a hyperthermophilic archaeon, Thermococcus nautili 30-1, that produces viral vesicles

Oberto J. et al.,
aUniversite Paris-Sud, CNRS, UMR8621, Institut de Genetique et Microbiologie, Orsay, France bFidelity Systems, Inc., Gaithersburg, Maryland, USA cInstitut Pasteur, Paris, France

... 16 ? 10 6 reads assembled with Velvet (3). Genome assembly was performed with Consed (4). The remaining gaps were filled using bacterial artificial chromosome (BAC) sequencing with Thermofidelase and Fimers (5). Genes were annotated using FGENESB (Softberry). ...


Journal of biotechnology
2014, 174, 14-15. DOI: 10.1016/j.jbiotec.2014.01.022

Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1

Jung J. H. et al.,
a Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea b Department of Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 580-185, Republic of Korea

... polymerase chain reactions. GeneMarkS ( Besemer et al., 2001), Glimmer 3.02 ( Delcher et al., 2007), and FgenesB (Softberry, Inc., Mount Kisco, NY) were used to predict open reading frames (ORFs). Their functions were verified ...


Journal of biotechnology
2014, 179, 15-16. DOI: 10.1016/j.jbiotec.2014.03.009

Draft genome sequence of Xanthomonas axonopodis pv. glycines 8ra possessing transcription activator-like effectors used for genetic engineering

Lee J. H. et al.,
a Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea b Department of Food and Animal Biotechnology, and Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea

... in Macrogen (Korea). ORF prediction was conducted using applications such as Glimmer3 (Delcher et al., 2007), GeneMarkS (Besemer et al., 2001), and FgenesB (Softberry, Inc., Mount Kisco, NY). Functional analysis of all ...


Archives of Virology
January 2014, Volume 159, Issue 1, pp 159-162 DOI: 10.1007/s00705-013-1776-6

Complete genome sequence of marine bacterium Pseudoalteromonas phenolica bacteriophage TW1

Hakdong Shin, Ju-Hoon Lee, Chi Sang Ahn, Sangryeol Ryu, Byung Cheol Cho
1. Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, 151-921, Korea 3. Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Korea

... using a GS-FLX pyrosequencer at Macrogen, Seoul, South Korea, and the qualified sequence reads were assembled using Newbler v2.3. The open reading frames (ORFs) in the genome were predicted using GeneMarkS [ 2 ], Glimmer3 [ 5 ], and FgenesB (Softberry, Inc., Mount ...


Archives of virology
2014, 1-4. DOI: 10.1007/s00705-014-2140-1

Complete genome sequence of enterobacteria phage 4MG, a new member of the subgroup "PVP-SE1-like phage" of the "rV5-like viruses"

Kim M., Heu S., Ryu S.
1. Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, South Korea 3. Microbial Safety Division, National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, South Korea

... A single contig assembled with quality-filtered reads was analyzed using the tools GeneMarkS [ 10 ], Glimmer 3.02 [ 11 ], and FgenesB (Softberry, Inc., NY, USA) for prediction of open reading frames (ORFs), BlastP [ 12 ], InterProScan [ 13 ], and NCBI Conserved Domain ...


AMB Express
2014, 4(1), 23. http://www.amb-express.com/content/4/1/23

Cloning, expression and characterization of a versatile Baeyer-Villiger monooxygenase from Dietzia sp. D5.

Bisagni, S., Hatti-Kaul, R., Mamo, G.
Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden

... D5 (unpublished data). Identification of ORFs and ana- lysis of the BVMO4 gene and its deduced protein se- quence was performed with CLCBio Main Workbench (Aarhus, Denmark) FGENESB (Soft Berry Mount Nysco, USA) and BLASTp at NCBI. ...


Environmental microbiology
2014, 16(5), 1334-1345. DOI:10.1111/1462-2920.12440

Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331

Fritsche K. et al.,
1 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands 2 BioDetection Systems b.v., Amsterdam, The Netherlands

... al., 2011). Gene colours indicate predicted function (see Supporting Information Table S1). Arrowed lines above the genes indicate operonic organization, as predicted by FgenesB (http://www.softberry.com). Black arrow heads ...


Functional & integrative genomics
2014, 1-10. DOI:10.1007/s10142-014-0375-2

Arsenic and cadmium are inhibitors of cyanobacterial dinitrogenase reductase (nifH1) gene

Singh, S., Shrivastava, A. K., Singh, V. K.
1. Molecular Biology Section, Laboratory of Algal Biology, Center of Advanced Study in Botany and Department of Bioinformatics, Banaras Hindu University and Shobhit University, Varanasi and Meerut, 221005, India 2. Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, 221005, India

... This was followed by FGeneSH B (Salamov and Solovyev 2000) (http://linux1.softberry.com/) to find out the bacterial operon and to predict transcription regulation within nifH1. Promoter analysis Virtual footprint 3.0 (Munch et al. 2005) (http://prodoric.tu-bs. ...


Microbial ecology
March 2014. DOI:10.1007/s00248-014-0388-3

Phylogenetic and Functional Analysis of Gut Microbiota of a Fungus-Growing Higher Termite: Bacteroidetes from Higher Termites Are a Rich Source of b-Glucosidase Genes

Zhang, M. et al.,
1. School of Life Sciences, East China Normal University, Shanghai, China 3. Key Laboratory of Insect Development and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

... 27, 28]. If 50 % ORFs of a contig were all binned to the same phylum, this contigs could be assigned to this phylum [21]. The ORFs of contigs were predicted by FgenesB (Softberry, Goteborg, Sweden). ?-Glucosidases were ...


PLOS ONE
December 12, 2013 DOI: 10.1371/journal.pone.0082985

Functional Environmental Screening of a Metagenomic Library Identifies stlA; A Unique Salt Tolerance Locus from the Human Gut Microbiome

Eamonn P. Culligan, Roy D. Sleator, Julian R. Marchesi, Colin Hill
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland, School of Microbiology, University College Cork, Cork, Ireland Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom, Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom

... platform on a titanium mini-run. Putative open reading frames were predicted using Softberry FGENESB bacterial operon and gene prediction software (available at www.softberry.com). Retrieved nucleotide and translated amino ...


J. Virol. November
2013 vol. 87 no. 21 11775-11786 DOI:10.1128/JVI.02173-13

Antirepression System Associated with the Life Cycle Switch in the Temperate Podoviridae Phage SPC32H

Minsik Kim and Sangryeol Ryu
Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea

... were assembled using the GS de novo assembler (v. 2.60), and the open reading frames (ORFs) that encode proteins of more than 35 amino acids in size were predicted using the software programs GeneMarkS (17), Glimmer 3.02 (18), and FgenesB (Softberry, Inc., Mount ...


MicrobiologyOpen
Volume 2, Issue 5, pages 717–724, October 2013 DOI:10.1002/mbo3.110

Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome

Chhabra et al.,
1 Department of Science and Health, Institute of Technology Carlow, Carlow, Ireland 2 Department of Microbiology, University College Cork, Cork, Ireland

... The gene calling of sequenced data was carried out using the Fgenesb annotator pipeline (Softberry Inc., Mount Kisco, NY) (http://linux1.softberry.com), GeneMark.hmm prediction tool (http://exon.gatech.edu/genemark/) (Besemer and Borodovsky 1999) and ORF Finder (open ...


MicrobiologyOpen
Volume 2, Issue 4, pages 674–683, August 2013 DOI:10.1002/mbo3.104

Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems

Vercammen et al.,
1Department of Bioengineering Sciences, Research group Microbiology and VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium 2Ecologie des Systemes Aquatiques, Universite Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium 3Genetique et Physiologie Bacterienne, Universite Libre de Bruxelles, IBMM-DBM, Gosselies, Belgium

... The sequences were assembled using CAP3 version 3 (available at Mobyle Pasteur: http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::cap3) and annotated by the free online program Softberry (http://linux1.softberry.com/berry.phtml?topic=fgenesb&group=programs&subgroup ...


Applied Microbiology and Biotechnology
July 2013 DOI:10.1007/s00253-013-5126-0

Molecular cloning and characterization of a novel acetylalginate esterase gene in alg operon from Sphingomonas sp. MJ-3

Yoo Jung Park, Yu Jeong Chu, Young Hee Shin, Eun Yeol Lee, Hee Sook Kim
1. Department of Food Science and Biotechnology, Kyungsung University, Busan, 608-736, Korea 2. College of Pharmacy, Kyungsung University, Busan, 608-736, Korea 3. Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do, 446-701, Korea

... The PCR primers used for screening and sequencing are listed in Table 1. The positive fosmid DNAs were sequenced, and then genes or operon were ana- lyzed by using fgenesb program (http://linux1.softberry.com/ berry.phtml) and ORF finder (http://www.ncbi.nlm.nih.gov ...


Genome Announc.
May/June 2013 vol. 1 no. 3 e00235-13 doi: 10.1128/genomeA.00235-13

Complete Genome Sequence of Xanthomonas citri subsp. citri Strain Aw12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium

Jalan et al.,
Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, Florida, USAa; Waksman Genomics Core Facility, Rutgers University, Busch Campus, Piscataway, New Jersey, USAb;

... between the 454 scaffolds. PCR amplification and Sanger sequencing were used to close the remaining gaps, and Softberry's FgenesB pipeline was used for finding protein coding sequences (CDS). The predicted CDS were ...


Genome Announc.
May/June 2013 vol. 1 no. 3 e00356-13 DOI:10.1128/genomeA.00356-13

Draft Genome Sequence of Methylobacterium mesophilicum Strain SR1.6/6, Isolated from Citrus sinensis

Almeida et al.,
Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Para, Brazila Departamento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Biomedicas II, Cidade Universitaria, Sao Paulo, Sao Paulo, Brazilb

... The functional annotation was performed using FgenesB (SoftBerry), RNAmmer (10), tRNAscan-SE (11), Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html), and InterProScan (12). In addition, manual annotation was also performed using Artemis software (13). ...


Genome Announc.
March/April 2013 vol. 1 no. 2 e00141-13 DOI:10.1128/genomeA.00141-13

Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T)

Golyshin et al.,
School of Biological Sciences, Bangor University, Bangor, Gwynedd, United Kingdoma; Max Planck Institute for Marine Microbiology, Bremen, Germanyb;

... The final assembly contains 12,110,290 short-insert library reads and provides 294? coverage of the genome. The automated genome annotation was performed at Fidelity Systems Ltd., using FgenesB 2.0 (SoftBerry, Inc., NY). ...


Archives of Virology
Volume 159, Issue 1 , pp 159-162 DOI:10.1007/s00705-013-1776-6

Complete genome sequence of marine bacterium Pseudoalteromonas phenolica bacteriophage TW1

Hakdong Shin, Ju-Hoon Lee, Chi Sang Ahn, Sangryeol Ryu, Byung Cheol Cho
1. Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, 151-921, Korea 3. Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Korea

... using a GS-FLX pyrosequencer at Macrogen, Seoul, South Korea, and the qualified sequence reads were assembled using Newbler v2.3. The open reading frames (ORFs) in the genome were predicted using GeneMarkS [ 2 ], Glimmer3 [ 5 ], and FgenesB (Softberry, Inc., Mount ...


Archives of Virology
Volume 158, Issue 10 , pp 2179-2183 DOI:10.1007/s00705-013-1700-0

Complete genome sequence analysis of bacterial-flagellum-targeting bacteriophage chi

Ju-Hoon Lee, Hakdong Shin, Younho Choi, Sangryeol Ryu
2. Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 446-701, Korea 1. Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, Korea

... Roche) at Macrogen, Inc. (Seoul, South Korea). Open reading frames (ORFs) were predicted using gene prediction programs such as Glimmer3 [ 13 ], GeneMarkS [ 3 ], and FgenesB (Softberry, Inc. Mount Kisco, NY, USA) and ...


Plant Science
Volume 211, October 2013, Pages 8–16 DOI:10.1016/j.plantsci.2013.06.008

Alterations in lignin content and phenylpropanoids pathway in date palm (Phoenix dactylifera L.) tissues affected by brittle leaf disease

Saidi et al.,
a Laboratoire des Biotechnologies Vegetales Appliquees a l’Amelioration des Cultures, Ecole Nationale d’Ingenieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038 Sfax, Tunisia b Centre de Recherches Phoenicicoles, 2260 Degache, Tunisia

.. and motif searches were performed on the protein sequences using Pfam (http://www.sanger. ac.uk/software/pfam), protein which did not exhibit the appropriate protein motif were re-predicted and manually corrected by using Fgenesh software (http://linux1.softberry.com/berry ...


Plasmid
Volume 70, Issue 2, September 2013, Pages 284–287 DOI:10.1016/j.plasmid.2013.06.001

pDB2011, a 7.6 kb multidrug resistance plasmid from Listeria innocua replicating in Gram-positive and Gram-negative hosts

David Bertsch, Janine Anderegg, Christophe Lacroix, Leo Meile, Marc J.A. Stevens
Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland

... Microsynth AG). Open reading frames (ORFs) were identified using the bacterial operon and gene prediction tool FGENESB (www.softberry.com). Annotation was done using BLAST (http://ncbi.nlm.nih.gov/blast/Blast.cgi). The ...


Appl. Environ. Microbiol.
March 2013 vol. 79 no. 5 1428-1435 DOI:10.1128/AEM.03291-12

Use of a Novel Escherichia coli-Leuconostoc Shuttle Vector for Metabolic Engineering of Leuconostoc citreum To Overproduce D-Lactate

Han Seung Chae a, Seung Hwan Lee b, Ju-Hoon Lee c, Si Jae Park d and Pyung Cheon Lee a
aDepartment of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, South Korea bChemical Biotechnology Research Center, Korea Research Institute of Chemical Technology (KRICT), Yuseong-gu, Daejeon, South Korea

... DNA and amino acid sequences were analyzed using the DNASTAR and Artemis12 software (20) programs. Prediction of open reading frames (ORFs) was conducted using the GeneMark (21) and FgenesB (Softberry, Mount Kisco, NY) programs. ...


J Gen Virol
November 2013 vol. 94 no. Pt 11 2569-2576 DOI:10.1099/vir.0.053991-0

Characterization and genomic analysis of two Staphylococcus aureus bacteriophages isolated from poultry/livestock farms

Hyunjin Yoon et al.,
1Department of Food Technology and Services, College of Health Industry, Eulji university, Seongnam 461-713, Korea 2Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Korea

... ORFs were predicted with Glimmer 3 (Delcher et al., 2007), GeneMarkS (Besemer et al., 2001) and FgenesB (http://linux1.softberry.com/berry.phtml). RBS finder (Suzek et al., 2001), which facilitates determination of the start codon of each ORF, ...


Appl. Environ. Microbiol.
June 2013 vol. 79 no. 12 3829-3838 DOI:10.1128/AEM.00581-13

Functional Screening of a Metagenomic Library Reveals Operons Responsible for Enhanced Intestinal Colonization by Gut Commensal Microbes

Yoon et al.,
Department of Microbiology,a Brain Korea 21 Project for Medical Sciences,b Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine,c Seoul, Republic of Korea

... Clustering of genes into an operon was performed using FGENESB, a program for the prediction of bacterial operons (SoftBerry, Mount Kisco, NY). The ORF map shown in Fig. 3A and B was constructed using CloneMap (ver. 2.11) software (CGC Scientific, Inc., Ballwin, MO). ...


Extremophiles
Volume 17, Issue 5 , pp 809-819 DOI:10.1007/s00792-013-0562-4

Characterization of a cold-adapted and salt-tolerant esterase from a psychrotrophic bacterium Psychrobacter pacificensis

Guojie Wu, Gaobing Wu, Tao Zhan, Zongze Shao, Ziduo Liu
1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China 2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

... The open reading frame (ORF) and the promoter region in the obtained DNA fragments were analyzed by FGENSB and BPROM (http://linux1.softberry.com/berry.phtml), amino acid alignments by BLASTP (http://www.ncbi.nlm.nih.gov/), and Signal peptide by the SignaIP 4.0 ...


Journal of Molecular Catalysis B: Enzymatic
Volume 98, 30 December 2013, Pages 119–126 DOI:10.1016/j.molcatb.2013.10.012

A novel esterase from a psychrotrophic bacterium Psychrobacter celer 3Pb1 showed cold-adaptation and salt-tolerance

Guojie Wu a, Shuo Zhang a, Houjin Zhang b, Shanshan Zhang a, Ziduo Liu a,
a State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China b School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430070, PR China

... of the esterase-encoding gene, est12, was carried out by Basic Local Alignment Search Tool (BLAST) program on the NCBI online database (http://www.ncbi.nlm.nih.gov), and the promoter region was analyzed by FGENSB and BPROM (http://linux1.softberry.com/berry.phtml ...


PloS one
March 01, 2013DOI: 10.1371/journal.pone.0057634

A Serratia marcescens PigP Homolog Controls Prodigiosin Biosynthesis, Swarming Motility and Hemolysis and Is Regulated by cAMP-CRP and HexS

Shanks et al.,
Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh Eye Center, Pittsburgh, Pennsylvania, United States of America Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

.. As noted above, the pigP gene is in a predicted operon with SMA3565-SMA3566 based on the alignment and proximity of open reading frames and Softberry FGENESB operon prediction software (http://linux1.softberry.com) (Figure 1B), however, this has not been previously ...


Archives of Virology
Volume 158, Issue 10 , pp 2101-2108 DOI:10.1007/s00705-013-1719-2

Characterization and complete genome sequence of a virulent bacteriophage B4 infecting food-borne pathogenic Bacillus cereus

Ju-Hoon Lee, Hakdong Shin, Bokyung Son, Sunggi Heu, Sangryeol Ryu
2. Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 446-701, Korea 1. Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, Korea

... Prediction of open reading frames (ORFs) was carried out using GeneMarkS [ 4 ], Glimmer v3.02 [ 11 ] and FgenesB software (Softberry, Inc. Mount Kisco, NY) and confirmed using RBSfinder (J. Craig Venter Institue, Rockville, MD). ...


Physiological and Molecular Plant Pathology
Volume 84, October 2013, Pages 61–69 DOI:10.1016/j.pmpp.2013.07.003

Modulated expression of ion transporters may be responsible for manganese deficiency in brittle leaf disease affected date palm (Phoenix dactylifera L.) trees

Saidi et al.,
a Laboratoire des Biotechnologies Vegetales Appliquees a l'Amelioration des Cultures, Ecole Nationale d'Ingenieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038 Sfax, Tunisia b Centre de Recherches Phoenicoles, 2260 Degache, Tunisia c Faculte des Sciences de Sfax, Route de Soukra Km 4, BP 1171, 3018 Sfax, Tunisia

... and motif searches were performed on the protein sequences using Pfam (http://www.sanger. ac.uk/software/pfam), protein which did not present the appropriate protein motif was re-predicted and manually corrected by using Fgenesh software (http://linux1.softberry.com/berry ...


American Journal of Molecular Biology
2013, 3, 115-130 DOI:10.4236/ajmb.2013.32016

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jose C. Jimenez-Lopez 1, Emma W. Gachomo 2,3, Sweta Sharma 2,3, Simeon O. Kotchoni 2,3
1Department of Biochemistry, Cell and Molecular Biology of Plants, Estacion Experimental del Zaidin, High Council for Scientific Research (CSIC), Granada, Spain 2Department of Biology, Rutgers University, Camden, USA 3Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, USA

Example of tools used for gene prediction are: 1) Glimmer, a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi), 2) FgenesB, a package developed by Soft- berry Inc. for automatic annotation of bacterial genomes (http://www.molquest.com/help/2.3/programs/FgenesB/about.html),


IJSEM
February 2013 vol. 63 no. Pt 2 526-532 DOI:10.1099/ijs.0.036947-0

Listeria fleischmannii sp. nov., isolated from cheese

Bertsch et al.,
1Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland 2Chemisches und Veterinaruntersuchungsamt Stuttgart (CVUAS), 70736 Fellbach, Germany

... The prediction tool FGENESB (Softberry) indicated the presence of eight open reading frames between prs and ldh, all showing the highest similarity (>50 %) with protein sequences from members of the genus Listeria (Fig. ...


Molecular & amp;Cellular Proteomics (mcp)
November 1, 2013 , 12, 3388-3397. DOI:10.1074/mcp.M112.027169

Proteogenomic Analysis of Bradyrhizobium japonicum USDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline

Kumar et al.,
From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India; §Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia

... FGENESB gene predictions were downloaded from (http://linux1.softberry.com/data/ annotation/bact/NC_004463.fna.ann.gz). ORF comparison across algorithms was performed using in-house scripts. Protein Functional Annotation. ...


Appl. Environ. Microbiol.
July 2013 vol. 79 no. 13 3967-3973 DOI:10.1128/AEM.00867-13

Biofilm Formation by Psychrobacter arcticus and the Role of a Large Adhesin in Attachment to Surfaces

Shannon M. Hinsa-Leasur a, Cassandra Koid a, James M. Tiedj b and Janna N. Schultzhaus a
Biology Department, Grinnell College, Grinnell, Iowa, USAa Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USAb

... with 64 bp separating the two genes. Based on results of the sequence analysis programs FGENESB and BPROM (SoftBerry), the Psyc_1602-encoding gene and cat1 reside in an operon. Located 379 bp downstream of cat1 ...


mcp
doi: 10.1074/mcp.M113.027318 mcp.M113.027318.

Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry

Zheng et al.,
1 Chinese Academy of Medical Sciences & Peking Union Medical College; 2 Chinese Academy of Medical Sc, China

... Gene prediction programs for prokaryotes were FgeneSB (http://linux1.softberry.com/berry. phtml?topic=fgenesb&group=programs&subgroup=gfindb) and GeneMark (http://exon.biology.gatech.edu/~genmark/gmhmm2_prok.cgi). Functional ...


J. Am. Chem. Soc.,
2013, 135 (47), pp 17906–17912 DOI: 10.1021/ja408683p

Discovery and Synthetic Refactoring of Tryptophan Dimer Gene Clusters from the Environment

Chang et al.,
Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States

... using 454 pyrosequencing technology (Roche). Clone assemblies were annotated using FGENESB (Softberry) or CloVR(15) for gene prediction and BLASTP (NCBI) for protein homology relationsips. The gene clusters reported ...


The Journal of Steroid Biochemistry and Molecular Biology
Volume 138, November 2013, Pages 41–53 DOI:10.1016/j.jsbmb.2013.02.016

Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains

Bragin et al.,
a Center of Innovations and Technologies “Biological Active Compounds and Their Applications”, Russian Academy of Sciences, Moscow 119991, Russian Federation b G.K.Skryabin Institute of Biochemistry & Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation

... weight matrices (PWM) were calculated from the known binding sites of transcription factors KstR [21] and KstR2 [39] and used for a search of similar sites in sequence 500 bp length upstream of operons found with the program FgenesB (http://linux1.softberry.com/berry.phtml ...


PNAS
February 12, 2013 vol. 110 no. 7 2478–2483, doi: 10.1073/pnas.1218073110

Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening

Fang-Yuan Chang and Sean F. Brady
Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065

... AB1091 was then annotated using FGENESB (Softberry) for gene prediction and BLASTP (National Center for Biotechnology Information) for protein homology searches (Fig. S9). Retrofitting and Conjugation of bor Gene Cluster-Containing Clone into S. albus. ...


BMC genomics
(2013). 14(1), 917. DOI:doi:10.1186/1471-2164-14-917

Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbiont of the green peach aphid, Myzus persicae

Jiang et al.,
1 Center for Computational Science, Miller School of Medicine, University of Miami, Coral Gables 33146, FL, USA 2 Department of Biology, University of Miami, Coral Gables 33146, FL, USA

... Genome annotation Gene models in the assembled genomes and plasmid scaffolds were predicted with FgenesB (www.softberry.com, utilizing the annotated genome of Buchnera aphidicola Bp (NC_004545) as a training set), GeneMark [62], and GLIMMER [63]. ...


Journal of Biomolecular Structure and Dynamics
(2013). 31(3), 342-350. DOI:

Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A

Lei, Y., Kang, S. K., Gao, J., Jia, X. S., & Chen, L. L.
a National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Center for Bioinformatics, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan , 430070 , P.R. China b College of Science, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan , 430070 , P.R. China

... BMC Bioinformatics, 11: 119 [PubMed] View all references) and FgenesB, (http://linux1.softberry.com/berry.phtml?topic=fgenesb&group=programs&subgroup= gfindb), respectively. Method for recognizing noncoding 'hypothetical ORFs'. ...


Frontiers in microbiology
(2013).4. DOI:10.3389/fmicb.2013.00340

Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria

Martinez, A., Ventouras, L. A., Wilson, S. T., Karl, D. M., & DeLong, E. F.
1Division of Biological Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA 2Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, USA

...The complete DNA sequence was assembled using Sequencher v. 4.10 (Gene Codes Corporation, Ann Arbor, MI) and annotated with FGENESB (Softberry) and BlastP (NCBI)....


Applied Microbiology and Biotechnology
Volume 97, Issue 18 , pp 8173-8182 DOI:10.1007/s00253-013-4927-5

Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing

Yan et al.,
1. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China 2. Biofuels institute, School of the Environment, Jiangsu University, Zhenjiang, 212013, Jiangsu, China

... whose GH activity was lost. ORFs were predicted by FgenesB (Softberry, Goteborg, Sweden), and a BLASTX search was performed against the NR database to access annotation information. Translated pro- tein sequences ...


AEM
Published ahead of print 14 December 2012, doi: 10.1128/AEM.03291-12

Metabolic Engineering to Overproduce D-Lactate by Leuconostoc citreum using a Novel E. coli-Leuconostoc Shuttle Vector

Han Seung Chae 1, Seung Hwan Lee 2, Ju-Hoon Lee 3, Si Jae Park 2 and Pyung Cheon Lee 1
1 Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, South Korea 2 Chemical Biotechnology Research Center, Korea Research Institute of Chemical Technology (KRICT), Yuseong-gu, Daejeon 305-600, South Korea

... 99 Prediction of open reading frames (ORFs) was conducted using GeneMark (5) and FgenesB 100 (Softberry, Mount Kisco, NY) programs. Gene annotation and similarity analysis were 101 performed using BLAST programs (2) from the National Center for Biotechnology 102 ...


FEMS Microbiology Letters
Volume 337, Issue 1, pages 1?9, December 2012 DOI: 10.1111/j.1574-6968.2012.02665.x

Novel traits of Trichoderma predicted through the analysis of its secretome

Irina S. Druzhinina 1,2, Ekaterina Shelest 3, Christian P. Kubicek 1,2,*
1 Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria 2 Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria

... Therefore, we applied the TMHMM Server v2.0 (http://www.cbs.dtu.dk/services/TMHMM/) to predict transmembrane helices in proteins, ProtComp, v8.0 (http://linux1.softberry.com/) and WolfPsort (http://wolfpsort.org/) both designed to predict the subcellular localization for animal ...


Journal of Biotechnology
Available online 28 November 2012

Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production

Soares et al.,
a CLIB Graduate Cluster Industrial Biotechnology, Centrum f?r Biotechnologie, Universit?t Bielefeld, 33615 Bielefeld, Germany b Institut f?r Genomforschung und Systembiologie, Centrum f?r Biotechnologie, Universit?t Bielefeld, 33615 Bielefeld, Germany

.. The complete genome sequence of C. pseudotuberculosis 258 was functionally annotated using the following softwares: FgenesB (http://linux1.softberry.com/); RNAmmer (Lagesen et al., 2007); tRNAscan-SE (Lowe and Eddy, 1997); InterproScan (Zdobnov and Apweiler, 2001 ...


Front Microbiol.
2012; 3: 185. DOI: 10.3389/fmicb.2012.00185

Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi

Liu et al.,
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 2Section for Marine Biology, Department of Biology, University of Copenhagen, Helsingor, Denmark

... assembly. The genome was annotated using a pipeline based on FGENESB software (Softberry, Inc., USA), Artemis (Sanger Institution, UK), and custom-made Perl scripts (ActivePerl; ActiveState Inc., Vancouver, BC, USA). ...


PLoS ONE
7(9): e43176. doi:10.1371/journal.pone.0043176

Theoretical Prediction and Experimental Verification of Protein-Coding Genes in Plant Pathogen Genome Agrobacterium tumefaciens Strain C58

Qian Wang, Yang Lei, Xiwen Xu, Gejiao Wang, Ling-Ling Chen
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China, Center for Bioinformatics, Huazhong Agricultural University, Wuhan, People's Republic of China

... Furthermore, potential new protein-coding genes that were not found in the RefSeq annotation were predicted by two ab initio gene finding programs, ie, Prokaryotic dynamic programming gene-finding algorithm (Prodigal) [21] and FgenesB (http://linux1.softberry.com/berry ...


Journal of Biomolecular Structure and Dynamics
2012 Aug 1. [Epub ahead of print] DOI: 10.1080/07391102.2012.698218

Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A.

Yang Lei a, Shou-Kai Kanga , Junxiang Gao b, Xi-Shuai Jia a & Ling-Ling Chen a
a National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Center for Bioinformatics, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, P.R. China b College of Science, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, P.R. China

... BMC Bioinformatics , 11: 119 View all references) and FgenesB, (http://linux1.softberry. com/berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb), respectively. Method for recognizing noncoding 'hypothetical ORFs'. ...


PLoS Negl Trop Dis.
2012 January; 6(1): e1471. doi: 10.1371/journal.pntd.0001471

Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence

Cejkova et al.,
1Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America

... bp. Gene identification and annotation. FgenesB (Softberry Inc., New York, USA), GeneMark [34] and Glimmer [35] were used independently for prediction of open reading frames (ORFs) in the Samoa D genome sequence. Visualization ...


PLoS One;
2011 May Journal Volume: 5; Journal Issue: 1;

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

Reddy et al.,

... the BLAST scores. After manual frameshift correction, genes were called using fgenesb (http:// www.softberry.com). For phylogenetic ... to Iodobacteriophage. Genes were predicted using fgenesV (www. softberry.com). Found at: doi ...


Food Microbiology
Volume 33, Issue 1, February 2013, Pages 124–130 DOI: 10.1016/j.fm.2012.09.008

Macedovicin, the second food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198

Georgalaki et al.,
a Laboratory of Dairy Research, Department of Food Science and Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece b Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France

... CAP3 (Huang and Madan, 1999). The region was annotated using heuristic GeneMark TM (Besemer and Borodovsky, 1999), FgenesB (http://www.softberry.com) and MetaGene annotator (Noguchi et al., 2006). At the same time ...


IJSEM
April 2012 DOI: 10.1099/ijs.0.036947-0

Listeria fleischmannii sp. nov., isolated from cheese

Bertsch et al.,
1 ETH Zurich; 2 CVUAS;

... JN118555). The 157 prediction tool FGENESB (Softberry, Inc.) indicated the presence of eight ORFs between prs and ldh, all 158 showing the highest homology (>50%) to protein sequences from Listeria species (Fig. 2). ORFB 159 ...


Journal of Molecular Evolution
Volume 74, Issue 3-4 , pp 187-205 DOI:10.1007/s00239-012-9498-z

Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens

Julia Krushkal, Yanhua Qu, Derek R. Lovley, Ronald M. Adkins
1. Department of Preventive Medicine, The University of Tennessee Health Science Center, 66 N. Pauline Blvd. Ste. 633, Memphis, TN, 38163, USA 2. Department of Microbiology, The University of Massachusetts, Amherst, MA, 01003, USA

... J Mol Evol 123 Page 5. predicted earlier and described previously (Krushkal et al. 2007; Mahadevan et al. 2008; Tran et al. 2008) using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc.; 2003–2009). ...


BMC Genomics
2012, 13:625 doi:10.1186/1471-2164-13-625

The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification

Maayer et al.,
1 Forestry and Agricultural Biotechnology Institute, Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa 2 Center for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa

... The CDS for complete LPP-1 sequences were downloaded from the National Center for Biotechnology Information (NCBI) database [63] and those encoded on the draft plasmids were predicted using FgenesB [64]....


Journal of Proteomics
Volume 77, 21 December 2012, Pages 357–371 DOI: 10.1016/j.jprot.2012.09.010

A comprehensive proteomic analysis of Mycobacterium bovis bacillus Calmette–Guerin using high resolution Fourier transform mass spectrometry

Zheng et al.,
MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China

... Two different gene prediction programs for prokaryotes, FgeneSB (http://linux1.softberry.com/ berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb) and GeneMark (http://exon.biology.gatech.edu/~genmark/gmhmm2_prok.cgi), supported the presence of this ...


MPMI
July 2012, Volume 25, Number 7 Pages 954-963 DOI: 10.1094/MPMI-11-11-0304

Nonlegume Parasponia andersonii Deploys a Broad Rhizobium Host Range Strategy Resulting in Largely Variable Symbiotic Effectiveness

Rik H. M. Op den Camp et al.,
1Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; 2Department of Agricultural Biotechnologies, Universita di Padova, Viale dell'Universita 16, 35020 Legnaro (Padova), Italy;

... Genes were predicted using FGENESB (Softberry, Mount Kisco, NY, USA), BASys (Van Domselaar et al. 2005), and manual annotation. Estimated full-length 16S rDNA and genes encoding proteins involved in Nod-factor biosynthesis were identified by BLAST searches. ...


J. Bacteriol. April
2012 vol. 194 no. 8 2041-2049 DOI doi: 10.1128/?JB.06637-11

Novel, Highly Specific N-Demethylases Enable Bacteria To Live on Caffeine and Related Purine Alkaloids

Ryan M. Summers et al.,
aDepartment of Chemical and Biochemical Engineering, University of Iowa, Iowa City, Iowa, USA bThe Center for Biocatalysis and Bioprocessing, University of Iowa, Coralville, Iowa, USA

... the supplemental material. Analyses of open reading frames (ORFs) were performed manually with the help of GeneMark.hmm for prokaryotes (23), FGENESB (Softberry, Inc., Mount Kisco, NY), and GLIMMER (9). Cloning and ...


J. Virol.
doi: 10.1128/?JVI.01987-12 October 2012 vol. 86 no. 20 11410-11411

Complete Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Bacteriophage My1

Dong Hwan Lee et al.,
aDivision of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea bDepartment of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea

... Quality filtered reads were assembled using a 454 Newbler 2.3 assembler. The open reading frames (ORFs) were predicted using the Glimmer v3.02 (3), GeneMarkS (2), and FgenesB (Softberry, Inc., Mount Kisco, NY) and then confirmed by the RBSfinder (17). ...


J. Bacteriol.
doi: 10.1128/?JB.01373-12 October 2012 vol. 194 no. 20 5718-5719

Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp162, Isolated from Camel

Syed Shah Hassan et al.,
aInstituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil bInstituto de Ciencias Biologicas, Universidade Federal do Para, Belem, PA, Brazil

... short reads (3) and manual curation. The functional annotation of the genome for open reading frame (ORF) prediction was performed using the software program FgenesB (Softberry). The software program RNAmmer (6) was ...


Appl Environ Microbiol.
August 2012, doi: 10.1128/?AEM.02120-12

Genomic and transcriptomic studies of an RDX-degrading actinobacterium

Hao-Ping Chen et al.,
1Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada 3U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, Mississippi

... 46 Biolabs). 47 Page 3. 3 Open reading frames (ORFs) were identified using the FGENESB software (Softberry Inc., 48 Mount Kisco, NY) and the RAST server (http://rast.nmpdr.org) (3). The genes that were 49 identified were ...


J. Virol.
doi: 10.1128/?JVI.01042-12 July 2012 vol. 86 no. 14 7713-7714

Complete Genome Sequence of Cronobacter sakazakii Temperate Bacteriophage phiES15

Ju-Hoon Lee b, Younho Choi a, Hakdong Shin a, Junghyun Lee a and Sangryeol Ryu a
aDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea bDepartment of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea

... The predictions of open reading frames (ORFs) were conducted using three major gene prediction programs, GeneMarkS (2), Glimmer3 (5), and FgenesB (Softberry, Inc., Mount Kisco, NY) and confirmed by ribosomal binding site analyses performed using RBS finder (J. Craig ...


J. Virol.
doi: 10.1128/?JVI.01283-12 August 2012 vol. 86 no. 16 8899-8900

Complete Genome Sequence of Phytopathogenic Pectobacterium carotovorum subsp. carotovorum Bacteriophage PP1

Ju-Hoon Lee et al.,
aDepartment of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea bDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea

... Korea). The open reading frames (ORFs) were bioinformatically predicted using Glimmer3 (4), GeneMarkS (2), and FgenesB (Softberry, Inc., Mount Kisco, NY) and confirmed by RBS finder (J. Craig Venter Institute, Rockville, MD). ...


J. Virol.
doi: 10.1128/?JVI.00706-12 June 2012 vol. 86 no. 11 6379-6380

Complete Genome Sequence of Bacillus cereus Bacteriophage PBC1

Minsuk Kong, Minsik Kim and Sangryeol Ryu
Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea

... The assembly of quality filtered reads was performed using GS De Novo Assembler (v. 2.6), and the open reading frames (ORFs) were predicted using the Glimmer 3.02 (4), GeneMark.hmm (3), and FgenesB (Softberry, Inc., Mount Kisco, NY) software. ...


J. Bacteriol.
doi: 10.1128/?JB.00824-12 August 2012 vol. 194 no. 16 4434-4435

Complete Genome Sequence of the Hyperthermophilic Archaeon Pyrococcus sp. Strain ST04, Isolated from a Deep-Sea Hydrothermal Sulfide Chimney on the Juan de Fuca Ridge

Jong-Hyun Jung et al.,
aDepartment of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea bDepartment of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA

... The open reading frames (ORFs) were predicted using GeneMarkS (2), Glimmer 3.02 (3), and FgenesB (Softberry, Inc., Mount Kisco, NY), and functional analyses of the predicted ORFs were conducted using BLASTP (1) and InterProScan (12). ...


J. Bacteriol.
doi: 10.1128/?JB.00461-12 July 2012 vol. 194 no. 13 3567-3568

Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama

Thiago Lopes et al.,
aInstituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Para, Brazil bInstituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil

... The following software programs were used in the automatic functional annotation of the genome: FgenesB (gene prediction; http://linux1.softberry.com/), RNAmmer (rRNA prediction) (3), tRNAscan-SE (tRNA prediction) (4), and Tandem Repeat Finder (repetitive DNA prediction ...


J. Bacteriol.
doi: 10.1128/?JB.01016-12 September 2012 vol. 194 no. 17 4769-4770

Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a Hydrothermal Vent

Jong-Hyun Jung et al.,
aDepartment of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, Republic of Korea bDepartment of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA

... Korea). GeneMarkS (2), Glimmer 3.02 (3), and FgenesB (Softberry, Inc., Mount Kisco, NY) were used to predict the open reading frames (ORFs) present. Their functions were verified using BLASTP (1) and InterProScan (15). ...


J. Bacteriol.
doi: 10.1128/?JB.00572-12 July 2012 vol. 194 no. 13 3561-3562

Genome Sequence of Bacillus licheniformis WX-02

Wuming Yangtse et al.,
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China

... Open reading frames were identified using Fgenesb (http://linux1.softberry.com/berry.phtml?topic= fgenesb&group=programs&subgroup=gfindb), Prodigal (http://compbio.ornl.gov/prodigal/), and Glimmer (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi) and ...


The ISME Journal
6, 1916-1925 (October 2012) | doi:10.1038/ismej.2012.38

Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome

Eamonn P Culligan, Roy D Sleator, Julian R Marchesi and Colin Hill

... FLX (Roche Applied Science) platform. Putative open reading frames were predicted using Softberry FGENESB bacterial operon and gene prediction software (Mavromatis et al., 2007). Retrieved nucleotide and translated amino ...


Front Microbiol.
2012; 3: 2. doi: 10.3389/fmicb.2012.00002

IncP-1e Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes

Holger Heuer et al.,
1Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kuhn-Institut, Braunschweig, Germany 2Department de Ciencias Biologicas, Universidad Adolfo Ibanez, Santiago, Chile

... to GenBank sequences. Additional searches for genes, operons, promoters, and terminators were done using FGENESB, BPROM, and FindTerm at www.softberry. com (Softberry, Mount Kisco, NY, USA). The sequence data ...


Extremophiles
September 2012, Volume 16, Issue 5, pp 715-726 DOI 10.1007/s00792-012-0467-7

Genome sequence of temperate bacteriophage Psymv2 from Antarctic Dry Valley soil isolate Psychrobacter sp. MV2

Tracy L. Meiring (1) I. Marla Tuffin (1) Craig Cary (2) Don A. Cowan (1)
1. Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Office 2117, Level 2 Life Sciences Building, Modderdam Rd, Bellville, 7535, South Africa 2. Department of Biological Sciences, University of Waikato, Hamilton, New Zealand

... Ab initio gene predictions were performed using GeneMark.hmm 2.0 (http://www.exon.biology. gatech.edu/heuristic_hmm2.cgi) (Besemer and Borodovsky 1999), fgenesv and fgenesb (http://www.linux1.softberry.com/berry.phtml) (Softberry, Mount Kisco, NY, USA) using the ...


AQUATIC MICROBIAL ECOLOGY
AQUATIC MICROBIAL ECOLOGY

Virus genes in Arctic marine bacteria identified by metagenomic analysis

Matthew T. Cottrell, David L. Kirchman
Matthew T. Cottrell, David L. Kirchman

... genomes EU795107, EU795222 to EU795255 and EU795278. Open reading frames were identified using the FGENESB (Softberry) web site (www.softberry.com) and then annotated using AutoFACT software (Koski et al. 2005 ...


Open Access Bioinformatics
2012:4 1–13 http://dx.doi.org/10.2147/OAB.S25500

reannotation of the Corynebacterium diphtheriae ncTc13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria

Vivian D’Afonseca et al.,
1Federal University of Minas gerais, Belo horizonte, Minas gerais, Brazil; 2Federal University of Pelotas, Pelotas, rio grande do sul, Brazil;

... Methods genome reannotation The reannotation procedures involved the use of several algorithms, in a multi-step process. Structural annotation was performed using the following software: FGENESB: bacterial operon and gene predictor (http://www.softberry. ...


World Journal of Microbiology and Biotechnology
August 2012 DOI 10.1007/s11274-012-1145-8

Cloning and biochemical characterization of a glucosidase from a marine bacterium Aeromonas sp. HC11e-3

Xiaoluo Huang et al.,
1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China 2. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, 361005, People’s Republic of China

... 1964). Sequence analysis Nucleotide sequencing was accomplished by the Gene- script Company (Nanjing, China) and the open reading frame (ORF) in the obtained DNA fragments was predicted by FGENESB in softberry database (http://linux1.soft berry.com/berry.phtml). ...


Virus Research
Volume 155, Issue 2, February 2011, Pages 433–439 DOI: 10.1016/j.virusres.2010.11.012

The genome sequence and proteome of bacteriophage ?CPV1 virulent for Clostridium perfringens

Volozhantsev et al.,
a State Research Center for Applied Microbiology & Biotechnology, Obolensk, Moscow Region, Russian Federation b Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, Athens, GA DOI:605, USA

... Protein-encoding genes (ORFs) were predicted using GeneMark.hmm for prokaryotes version 2.4 (http://opal.biology.gatech.edu/GeneMark; Lukashin and Borodovsky, 1998) and SoftBerry FGENESB (http://linux1.softberry.com/berry.phtml; Mount Kisco, NY, USA) programs. ...


J. Bacteriol.
June 2011 vol. 193 no. 12 3158-3159 DOI: 10.1128/JB.00310-11

Genome Sequence of Rhizobium etli CNPAF512, a Nitrogen-Fixing Symbiont Isolated from Bean Root Nodules in Brazil

Maarten Fauvart †, Aminael Sanchez-Rodriguez †, Serge Beullens, Kathleen Marchal and Jan Michiels *
Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, BE-3001 Heverlee, Belgium

... average length). Protein-coding genes were predicted using the Softberry FgenesB algorithm (http://linux1.softberry.com/all.htm). Functional annotation was performed by BLAST searches against the GenBank database. The ...


Appl. Environ. Microbiol
September 2011 vol. 77 no. 17 6189-6198 DOI: 10.1128/AEM.00377-11

Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14

Ganyu Gu 1, Leif Smith 2,*, Aixin Liu 1,3 and Shi-En Lu 1,*
1Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 32 Creelman St., Mississippi State, Mississippi 39762 2Department of Biological Sciences, Texas A&M University, College Station, Texas 77843

... Open reading frames (ORFs) and genes were subsequently predicted by the Softberry FGENESB program (Softberry, Inc., Mount Kisco, NY), and the identified ORFs and genes were analyzed using Blastx in the NCBI database. ...


FEMS Microbiology Letters
Volume 318, Issue 1, pages 18–26, May 2011 DOI: 10.1111/j.1574-6968.2011.02232.x

Comparative and evolutionary analysis of plasmid pREN isolated from Lactobacillus rennini, a novel member of the theta-replicating pUCL287 family

Asteri, I.-A., Papadimitriou, K., Boutou, E., Pot, B., Vorgias, C. E. and Tsakalidou, E.
1 Laboratory of Dairy Research, Department of Food Science and Technology, Agricultural University of Athens, Athens, Greece 2 Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece

... In order to identify potential protein encoding segments, three open reading frames (orfs) prediction programs were used: heuristic genemark™ (Besemer & Borodovsky, 1999), fgenesb (http:www.softberry.com) and metageneannotator (Noguchi et al., 2006). ...


J. Bacteriol.
October 2011 vol. 193 no. 20 5707-5715 DOI: 10.1128/JB.05426-11

Long-Chain N-Acyl Amino Acid Synthases Are Linked to the Putative PEP-CTERM/Exosortase Protein-Sorting System in Gram-Negative Bacteria

Jeffrey W. Craig, Marisa A. Cherry and Sean F. Brady
Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10065

... GS FLX Titanium XLR70; Roche Diagnostics Corp.) and standard Sanger-type sequencing (Table 1). Sequences from each respective eDNA insert were analyzed for putative open reading frames (ORFs) using GLIMMER, version 3.02 (14), and SoftBerry FGENESB (bacterial ...


FEMS Microbiology Letters
317: 83–92. doi: 10.1111/j.1574-6968.2011.02218.x

Characterization of a functional toxin–antitoxin module in the genome of the fish pathogen Piscirickettsia salmonis.

Gomez, F. A., Cardenas, C., Henriquez, V. and Marshall, S. H.
1 Laboratorio de Genetica e Inmunologia Molecular, Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile 2 Nucleo Biotecnologia Curauma (NBC), PUCV, Curauma, Valparaiso, Chile

... Sequence analysis. The DNA sequenced data were analysed with the softberry server software (http://linux1.softberry.com/berry.phtml) using the algorithms, FgenesB (to find possible ORFs in the sequences), and Bprom (to search for putative bacterial promoters). ...


Antonie van Leeuwenhoek
Volume 99, Issue 2 , pp 409-416 DOI: 10.1007/s10482-010-9476-7

Characterization of transcription within sdr region of Staphylococcus aureus

Izabela Sitkiewicz, Ireneusz Babiak, Waleria Hryniewicz
1. Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chelmska 30/34, Warszawa, Poland 2. Department of Orthopedics and Traumatology of Locomotory System, Medical University of Warsaw, Warsaw, Poland

... The presence of putative promoters and transcrip- tional organization of the sdr region was detected using the BPROM and FGENESB algorithms (www. softberry.com) based on region 611262 bp–623152 bp (GeneBank number CP000730.1) of the S. aureus subsp. ...


FEMS Microbiology Letters
314: 18–24. doi: 10.1111/j.1574-6968.2010.02132.x

ISPsa2, the first mobile genetic element to be described and characterized in the bacterial facultative intracellular pathogen Piscirickettsia salmonis.

Marshall, S. H., Henriquez, V., Gomez, F. A. and Cardenas, C.
1 Laboratorio de Genetica e Inmunologia Molecular, Instituto de Biologia, Facultad de Ciencias, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile 2 NBC, Nucleo de Biotecnologia Curauma, Curauma, Valparaiso, Chile

... sequencing by Macrogen Inc. (Korea). Sequence analysis. The DNA sequence data were analyzed with softberry server software (http://linux1.softberry.com/berry.phtml) using the FgenesB and Bprom algorithms. FgenesB is a suite ...


J. Bacteriol.
January 2011 vol. 193 no. 1 323-324 DOI: 10.1128/JB.01211-10

Complete Genome Sequence of Corynebacterium pseudotuberculosis I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis

Silva et al.,
1Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, PA, Brazil 2Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil

... For structural annotation, the following software programs were employed: FgenesB, a gene predictor (http://www.softberry.com); RNAmmer, an rRNA predictor (4); tRNAscan-SE, a tRNA predictor (5); and Tandem Repeats Finder, a repetitive-DNA predictor (http://tandem.bu.edu ...


Microbiology
March 2011 vol. 157 no. 3 636-647 DOI: 10.1099/mic.0.046045-0

cAMP receptor protein (CRP) positively regulates the yihU–yshA operon in Salmonella enterica serovar Typhi

Villarreal et al.,
1Laboratorio de Microbiologia Molecular, Departamento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile 2Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico

... In silico analyses to evaluate the transcriptional organization of the yihU–yshA cluster were performed using the fgenesb program (http://www.softberry.com), the ORF program (http://bioinformatics.biol.rug.nl/), and the EcoCyc (Keseler et al., 2009) and Prodoric databases ...


J. Bacteriol.
December 2011 vol. 193 no. 24 7025-7026 doi: 10.1128/JB.06293-11

Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya

Cerdeira et al.,
1Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Brazil 2Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

... The structural annotation was done automatically by a multipronged approach using the following programs: for gene prediction, FgenesB (http: //www.softberry.com); for rRNA prediction, RNAmmer (5); for tRNA prediction, tRNA-scan-SE (6); and for repetitive DNA prediction ...


J. Bacteriol.
doi: 10.1128/JB.05854-11 October 2011 vol. 193 no. 20 5871-5872

Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T

Stynen et al.,
1Laboratorio de Bacteriologia Aplicada, Departamento de Medicina Veterinaria Preventiva, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil 2CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, VIC, Australia

... fetus 82-40 (NC_008599) as the scaffold. Structural annotation was performed by the following predictors: for genes, FgenesB (SoftBerry); for rRNA, RNAmmer (10); for tRNA, tRNAscan-SE (12); and for repetitive DNA, Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html). ...


International Journal of Food Microbiology
Volume 144, Issue 3, 5 January 2011, Pages 400–405 DOI: 10.1016/j.ijfoodmicro.2010.10.026

Genome analysis of Lactobacillus fermentum temperate bacteriophage ÔPYB5

Xiuhong Zhang a, b, Shaohua Wang a, Tingting Guo a, Jian Kong a
a State Key Laboratory of Microbial Technology, Shandong University, Jinan, China 250100 b College of Life Science, Shanxi Normal University, Linfen, China 041000

... Sequence analysis was performed using BlastX, BlastN, BlastP and FastA programs. Putative ORFs were also identified using GenMark (http://opal.biology.gatech.edu/GeneMark/ gmhmm2_prok.cgi) and fgenesb software (http://www.softberry.com/). ...


Journal of Genetics and Genomics
Volume 38, Issue 6, 20 June 2011, Pages 243–252 DOI: 10.1016/j.jgg.2011.04.006

Genome

Xiao-Yan You et al.,
a State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China b Shanghai MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China

... http://www.phrap.org). 2.4. Sequence analysis. The Glimmer 3.02 (Delcher et al., 2007) and FgeneSB programs (http://www.softberry.com/) were used to predict the positions of open reading frames (ORFs). Protein function was ...


Environmental Microbiology Reports
3: 203–210. doi: 10.1111/j.1758-2229.2010.00209.x

Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis.

Cusano et al.,
1 INRA, UMR1136 INRA-Nancy Universite, «Interactions Arbres/Micro-organismes», Centre de Nancy, IFR110, 54280 Champenoux, France. 2 Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.

... partially conserved. Figure 2. Alignment by tblastx of the P. fluorescens BBc6R8 and SBW25 T3SSs, generated using WebACT (Carver et al., 2005). BBc6R8 genes were predicted using FgenesB (Softberry). Regions of high ...


Appl. Environ. Microbiol.
July 2011 vol. 77 no. 13 4293-4302 doi: 10.1128/AEM.00195-11

Regulation of the Edwardsiella ictaluri Type III Secretion System by pH and Phosphate Concentration through EsrA, EsrB, and EsrC

Matthew L. Rogge 1 and Ronald L. Thune 1,2
1Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803 2Department of Veterinary Science, Louisiana State University Agricultural Center, Louisiana State University, Baton Rouge, Louisiana 70803

... Target amplicons, their operons, and their gene-specific primers are listed in Table 2. Putative operons were identified by using FGENESB (SoftBerry, Inc., Mount Kisco, NY), and transcriptional linkages were subsequently confirmed by reverse transcription-PCR (RT-PCR) using ...


The ISME Journal
(2012) 6, 146–157; doi:10.1038/ismej.2011.88; published online 21 July 2011

Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

Dawn E Holmes 1,2,3, Carla Risso 1,3, Jessica A Smith 1 and Derek R Lovley 1
1Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA 2Department of Physical and Biological Sciences, Western New England College, Springfield, MA, USA

... Operon organization of the F. placidus genome was predicted using the commercial version of the FGENESB software (V Solovyev and A Salamov, unpublished data; Softberry Inc., Mount Kisco, NY, USA; 2003–2009), as previously described for the genomes of various ...


J. Bacteriol.
November 2011 vol. 193 no. 22 6342-6357 doi: 10.1128/JB.05777-11

Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificity

Jalan et al.,
1Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida 33850 2Interdisciplinary Center for Biotechnology Research, 2033 Mowry Road, University of Florida, Gainesville, Florida 32611

... validation. Annotation and curation.Coding genes were identified using Softberry's FgenesB suite of bacterial operon- and gene-finding programs, based on the Markov chain model prediction algorithm at ICBR, UF (108). Predicted ...


Molecular Microbiology
(2011), 80: 951–965. doi: 10.1111/j.1365-2958.2011.07622.x

Anti-activator QslA defines the quorum sensing threshold and response in Pseudomonas aeruginosa.

Seet, Q. and Zhang, L.-H.
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673.

... aa in the Pseudomonas Genome Database (http://www.pseudomonas.com), but our in silico analysis predicted a translational start site at 27 bp downstream of the original annotated start site and the open reading frame would generate a 104 aa protein (FGENESB, Softberry). ...


PLoS ONE
(2011) 6(2): e16626. doi:10.1371/journal.pone.0016626

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis.

Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR
Howard Hughes Medical Institute, Department of Bioengineering, Stanford University, Stanford, California, United States of America Department of Environmental Earth System Science, Stanford University, Stanford, California, United States of America

... Gene prediction was carried out on the N. limnia assembly using the FgenesB platform (Softberry, Inc.), which called 2171 genes, including 2047 protein-coding ORFs, 74 pseudogenes, and 50 RNA genes [Table 2]. In total, 83.4% of the assembled bases were predicted to ...


Appl. Environ. Microbiol.
September 2011 vol. 77 no. 18 6663-6673 doi: 10.1128/AEM.05111-11

Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont "Candidatus Liberibacter asiaticus" as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats

Zhou et al.,
1University of Florida, IFAS-IRREC, Ft. Pierce, Florida 34945 2USDA-ARS-USHRL, Ft. Pierce, Florida 34945

... Bioinformatics and phylogenetic analysis.Tandem repeats finder version 4.04 (4) was used to find repeats in hyv I and hyv II sequences. Bacterial gene predictions were carried out using FGENESB software (SoftBerry Inc., Mount Kisco, NY). ...


The ISME Journal
(2011) 5, 1253–1261; doi:10.1038/ismej.2011.15; published online 3 March 2011

Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment

Gaze et al.,
1School of Life Sciences, University of Warwick, Coventry, Warwickshire, UK 2University of Birmingham, School of Immunity and Infection, Edgebaston, Birmingham, UK

... first nucleotide BLAST (basic local alignment search tool; National Center for Biotechnology Information (NCBI)) was used to check for homology with previously reported attC regions, then the NCBI ORF finder (open reading frame finder) and FGENESB (Softberry, Mount Kisco ...


Microbiology
April 2011 vol. 157 no. 4 1229-1239 DOI: 10.1099/mic.0.044669-0

Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system

Carina Holkenbrink, Santiago Ocon Barbas, Anders Mellerup, Hiroyo Otaki† and Niels-Ulrik Frigaard
Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark

... Black arrows indicate binding of primers for PCR and sequencing. Prediction of promoters and terminators was done using fgenesb software (http://linux1.softberry. com/berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb). ...


OMICS: A Journal of Integrative Biology.
July/August 2011, 15(7-8): 495-506. doi:10.1089/omi.2010.0117.

Genome Diversity of the TetR Family of Transcriptional Regulators in a Metal-Reducing Bacterial Family Geobacteraceae and Other Microbial Species

Krushkal et al.,
1Department of Preventive Medicine, the University of Tennessee Health Science Center, Memphis, Tennessee. 2Bioinformatics Program, the University of Memphis, Memphis, Tennessee.

... Operon organization of the Geobacteraceae genomes was predicted using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc., 2003–2009), as described earlier (Krushkal et al., 2007; Mahadevan et al., 2008; Tran et al ...


Front Microbiol.
2011; 2: 116. DOI: 10.3389/fmicb.2011.00116

Mechanisms and Evolution of Oxidative Sulfur Metabolism in Green Sulfur Bacteria

Lea H. Gregersen, 1,† Donald A. Bryant, 2 and Niels-Ulrik Frigaard 1,*
1Department of Biology, University of Copenhagen, Helsingor, Denmark 2Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA

... the following software: MEGA 4 (sequence alignment and phylogenetics 6 ; Tamura et al., 2007), Artemis 12.0 (sequence viewing and manipulation; Wellcome Trust Sanger Institute, Hinxton, UK 7 ; Carver et al., 2008), FGENESB (sequence annotation; Softberry, Mount Kisco ...


PLoS ONE 6
2011, (5): e20095. doi:10.1371/journal.pone.0020095

Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System.

Skennerton et al.,
Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland, Australia, Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia

... Annotation of phage contigs. Open Reading Frames (ORFs) were predicted using FGENESB (www.softberry.com) to call the position of the ORFs. Each ORF was extracted and compared against the NCBI non-redundant protein database (nr) using BLASTp. ...


BMC Genomics
2011, 12:576 doi:10.1186/1471-2164-12-576

Comparative genomics of the type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins

Maayer et al.,
1 Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa 2 Agroscope Changins-Wadenswil ACW, Division of Plant Protection, Wadenswil, Switzerland

...Proteins encoded in the vgrG and hcp islands were identified using the FgenesB [56] and Orf finder...


International Journal of Food Microbiology
Volume 146, Issue 1, 15 March 2011, Pages 23–30 DOI: 10.1016/j.ijfoodmicro.2011.01.033,

cspB encodes a major cold shock protein in Clostridium botulinum ATCC 3502

Soderholm et al.,
a Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland b Centre for Biomolecular Sciences, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK

... 2007). Based on the prediction made with FGENESB bacterial operon and gene prediction tool (http://www.softberry.com), none of the genes is located in an operon. The genes next to the three csp genes are presented in Fig. 3. ...


BMC Microbiology
2011, 11:25 doi:10.1186/1471-2180-11-25

Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate

Camilli et al.,
1 Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanita, Rome, Italy 2 Italian National Research Council, Institute for Biomedical Technologies, Milan, Italy

...The generated sequences were annotated identifying coding genes by cross prediction from the FGENESB package http://www.softberry.com/ webcite, th...


Molecular & Cellular Proteomics
December 1, 2011 , 10, M111.011627. doi: 10.1074/mcp.M111.011627

Proteogenomic Analysis of Mycobacterium tuberculosis By High Resolution Mass Spectrometry

Kelkar et al.,
From the ‡Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India, §Amrita School of Biotechnology, Amrita University, Kollam 690 525, India

...Two gene prediction programs, FgeneSB and GeneMark as well as the Orfind tool from NCBI were used to find ORFs in the region to which these GSSPs were mapped (18, 19)....


PLoS ONE
2011, 6(4): e18551. doi:10.1371/journal.pone.0018551

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

Ruiz et al.,
1Research Center Rene? Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil, 2Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil

...Structural annotation was performed using the following software: FgenesB: gene predictor (www.softberry.com); R...


PNAS
September 28, 2010 vol. 107 no. 39 16828-16833 doi: 10.1073/pnas.1011557107

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics

Wenjun Zhang a,b, Bohdan Ostash c,d, and Christopher T. Walsh a,1
a Department of Biological Chemistry and Molecular Pharmacology and c Department of Microbiology and Moledular Genetics, Harvard Medical School, Boston, MA 02115; b Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720

... 2.2.18) downloaded from the National Center for Biotechnology Information Web site. ORFs were detected and analyzed using online program FGENESB (Softberry), and the putative roles of the proteins were assigned using protein–protein BLAST and Pfam analysis. ...


The ISME Journal
8 July 2010, doi:10.1038/ismej.2010.94

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

Melissa Beth Duhaime, Antje Wichels, Jost Waldmann, Hanno Teeling and Frank Oliver Glockner

... hmm (prokaryotic version using bacterial or archaeal genetic code, precomputed Pseudoalteromonas haloplanktis chromosome 1 model and default settings) (Besemer et al., 2001) and (ii) FGENESB (generic bacterial model, default settings; Softberry, Mount Kisco, NY, ... 


Appl. Environ. Microbiol.
doi:10.1128/AEM.00928-10

Functionality of sortase A in Lactococcus lactis

Dieye et al.,
INRA, UMR1319 Micalis, Batiment 222, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands

... SrtA is annotated 59 as a putative 287 amino acid protein. 60 In silico analysis of the srtA locus using the gene prediction server FGENESB (Softberry) 61 (http://linux1.softberry.com/berry.phtml? topic=fgenesb&group=programs&subgroup=gfindb) indicated a 62 ... 


Applied and Environmental Microbiology
March 2010, p. 1633-1641, Vol. 76, No. 5, doi:10.1128/AEM.02169-09

Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria

Jeffrey W. Craig, Fang-Yuan Chang, Jeffrey H. Kim, Steven C. Obiajulu, and Sean F. Brady
Howard Hughes Medical Institute, Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065

... Each cosmid was sequenced by 454 pyrosequencing, and the sequences were analyzed for putative open reading frames (ORFs) using GLIMMER3.02 (12) and SoftBerry FGENESB: Bacterial Operon and Gene Prediction Program (http://linux1.softberry.com/berry.phtml?topic ... 


Journal of Bacteriology
May 2010, p. 2583-2595, Vol. 192, No. 10 doi:10.1128/JB.01526-09

The Actinomycin Biosynthetic Gene Cluster of Streptomyces chrysomallus: a Genetic Hall of Mirrors for Synthesis of a Molecule with Mirror Symmetry

Ullrich Keller,* Manuel Lang, Ivana Crnovcic, Frank Pfennig,§ and Florian Schauwecker
Institut fur Chemie, Arbeitsgruppe Biochemie und Molekulare Biologie, Technische Universitat Berlin, Franklinstrasse 29, D-10587 Berlin-Charlottenburg, Germany

... Open reading frames (ORFs), operons, transcriptional start points, promoters, and terminators were identified using various computer programs such as FGENES-B (Softberry Inc.), SAK (21), BPROM (Softberry Inc.), and FindTerm (Softberry Inc.). ... 


Journal of Microbiology
doi:10.1007/s10482-010-9476-7

Characterization of transcription within sdr region of Staphylococcus aureus

Izabela Sitkiewicz 1 , Ireneusz Babiak 2 and Waleria Hryniewicz 1
(1)  Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chelmska 30/34, Warszawa, Poland (2)  Department of Orthopedics and Traumatology of Locomotory System, Medical University of Warsaw, Warsaw, Poland

... The presence of putative promoters and transcrip- tional organization of the sdr region was detected using the BPROM and FGENESB algorithms (www. softberry.com) based on region 611262 bp–623152 bp (GeneBank number CP000730.1) of the S. aureus subsp. ... 


International Journal of Food Microbiology
Volume 141, Issue 3, 15 July 2010, Pages 222-228

Characterization of pLAC1, a cryptic plasmid isolated from Lactobacillus acidipiscis and comparative analysis with its related plasmids

Asteri et al.,
a Laboratory of Dairy Research, Department of Food Science and Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece b Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupolis-Zographou, 157 84 Athens, Greece

... 1999). Ab initio orf finding was performed using several bioinformatics tools, including heuristic GeneMark (Besemer & Borodovsky, 1999), FGENESB (www.softberry.com) and MetaGeneAnnotator (Noguchi et al., 2006). Only ...


Journal of Bacteriology
July 2010, p. 3337-3344, Vol. 192, No. 13 doi:10.1128/JB.00274-10

Treponema denticola PrcB Is Required for Expression and Activity of the PrcA-PrtP (Dentilisin) Complex{triangledown}

Godovikova et al.,
Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan

... Annotation of the prcB open reading frame was done using the FGENESB algorithm trained to the T. denticola genome sequence (Softberry, Inc., Mt. Kisco, NY). A predicted 70 class promoter upstream of prcB was identified using BPROM software (Softberry, Inc., Mt. ... 


Applied and Environmental Microbiology
October 2010, p. 6769-6777, Vol. 76, No. 20 doi:10.1128/AEM.00343-10

Comparative Analysis of Acidobacterial Genomic Fragments from Terrestrial and Aquatic Metagenomic Libraries, with Emphasis on Acidobacteria Subdivision 6

Anna M. Kielak, 1 Johannes A. van Veen, 1,2 and George A. Kowalchuk 1,3*
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 40, 6666 ZG Heteren, Netherlands,1 Institute of Biology Leiden University, P.O. Box 9516, 2300 RA Leiden, Netherland,2

...Annotation and sequence properties. Open reading frames (ORFs) were assigned using the GLIMMER (12) and FGENESB (http://linux1.softberry.com) software tools. ... Searches for GC islands were performed using CpGFinder (http://linux1.softberry.com). ... .


J Microbiol.
2010 Jun;48(3):318-24. Epub 2010 Jun 23.

Cel8H, a novel endoglucanase from the halophilic bacterium Halomonas sp. S66-4: molecular cloning, heterogonous expression, and biochemical characterization

Huang et al.,
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.

... The open reading frame (ORF) and the promoter region in the obtained DNA fragments were predicted using FGENSB and BPROM (http://linux1.softberry.com/berry.phtml). ... Genes in the 3.3 kb DNA fragment were predicted using FGENSB in the softberry website. ... 


PLoS ONE
2010, 5(9): e13092. doi:10.1371/journal.pone.0013092

Functional Metagenomics: A High Throughput Screening Method to Decipher Microbiota-Driven NF-?B Modulation in the Human Gut

Lakhdari et al.,
INRA, UMR 1319 Micalis, Jouy-en-Josas, France, 2 LibraGen S.A., Toulouse, France

... Evry, France). The sequence is available on GenBank (accession number HQ231916). Potential transcription units were detected using SoftBerry's software FGENESB (http://linux1.softberry.com/berry.phtml). Potential ORFs ... 


Microbiology
2010, DOI 10.1099/mic.0.046045-0

The cAMP-Receptor Protein (CRP) positively regulates the yihU-yshA operon in Salmonella enterica serovar Typhi

Villarreal et al.,
1 Universidad Andres Bello; 2 Universidad Nacional Autonoma de Mexico

... In silico analyses, to evaluate the transcriptional organization of the yihU-yshA cluster, were performed using the FGENESB program (http://www.softberry.com), the ... (http://www.softberry. com), programs which recognize and identify DNA patterns to ...


Applied and Environmental Microbiology
October 2010, p. 6329-6337, Vol. 76, No. 19, doi:10.1128/AEM.01217-10

Functional Characterization of pGKT2, a 182-Kilobase Plasmid Containing the xplAB Genes, Which Are Involved in the Degradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by Gordonia sp. Strain KTR9

Indest et al.,
U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, Mississippi,1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada2

... 232 233 Open reading frames (ORFs) were identified using FGENESB program (Softberry Inc., 234 ... pGKT2 were analyzed for bacterial promoter elements and Rho independent terminator 236 sequences using BPROM and FindTerm programs (Softberry Inc.). ... 


Microbiology
2010, DOI 10.1099/mic.0.041491-0

ccrABEnt serine recombinase genes are widely distributed in the Enterococcus faecium and Enterococcus casseliflavus species-groups and expressed in E. faecium

Bjorkeng et al.,
1 University of Tromso; 2 University Hospital of North-Norway; 3 CODA-CERVA-VAR; 4 UMCU

... 2010.02.08), Gene Mark (v2.4) (Besemer & Borodovsky, 1999), FGENESB 113 (www.softberry. com 2010.02.08), and ARTEMIS (Wellcome Trust Genome Campus, 114 Hinxton, Cambridge, UK). Pairwise comparison and multiple sequence alignments were 115 ... 


International Journal of Food Microbiology
Volume 144, Issue 3, 5 January 2011, Pages 400-405 doi:10.1016/j.ijfoodmicro.2010.10.026

Genome analysis of Lactobacillus fermentum temperate bacteriophage FPYB5

Xiuhong Zhang a, b, Shaohua Wang a, Tingting Guo a and Jian Kong a
a State Key Laboratory of Microbial Technology, Shandong University, Jinan, China 250100 b College of Life Science, Shanxi Normal University, Linfen, China 041000

... Sequence analysis was performed using BlastX, BlastN, BlastP and FastA programs. Putative ORFs were also identified using GenMark (http://opal.biology.gatech.edu/GeneMark/ gmhmm2_prok.cgi) and fgenesb software (http://www.softberry.com/). ...


PLoS ONE
5(1): e8812. doi:10.1371/journal.pone.0008812

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

Allgaier et al.,
1 Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America, 2 Department of Biological and Agricultural Engineering, University of California Davis, Davis, California, United States of America

.. scores. After manual frameshift correction, genes were called using fgenesb (http://www.softberry.com). For ... Iodobacteriophage. Genes were predicted using fgenesV (www.softberry.com). (1.12 MB EPS). Figure S2. Correspondence ... 


Applied and Environmental Microbiology
June 2010, p. 3715-3722, Vol. 76, No. 11, doi:10.1128/AEM.02753-09

Characterization of Genes Responsible for the CO-Linked Hydrogen Production Pathway in Rubrivivax gelatinosus

Vanzin et al.,
National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401

... as noted above. Sequence analysis. Open reading frames (ORFs) were predicted with FGENESB (Softberry, Inc.) and SYCO (synonymous codon usage Gribskov statistic plot) trained on the Rx. gelatinosus codon usage table ... 


BMC Genomics
2010, 11:350doi:10.1186/1471-2164-11-350

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

Kumar et al.,
1 Department of Basic sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA 2 Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA

... potential to code smaller proteins. Further analysis of the DNA sequence in these regions using FGENESB gene prediction tool (www.softberry.com) identified the presence of smaller ORF (open reading frame). We did not find any predicted promoter sequences in the ... 


Journal of Proteomics
Volume 73, Issue 5, 10 March 2010, Pages 917-931 doi:10.1016/j.jprot.2009.12.005

Proteome of Gluconacetobacter diazotrophicus co-cultivated with sugarcane plantlets

dos Santos MF, Muniz de Padua VL, de Matos Nogueira E, Hemerly AS, Domont GB.
a Federal University of Parana, Campus Palotina, Brazil b Federal University of Rio de Janeiro, Laboratory of Protein Chemistry/Rio de Janeiro Proteomics Network, Department of Biochemistry, Institute of Chemistry/Brazil

... To understand the biological roles of identified proteins, the web version of FGENESB Suite of Bacterial Operon and Gene Finding Programs (http://www.softberry.com/) was used for the analysis of the genetic organization around the ORFs of the differentially expressed proteins ... 


BMC Genomics.
2010 Sep 8;11:489.

Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans

Kittichotirat W, Bumgarner R, Chen C.
Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA, USA.

... fragments. Similar results were obtained using FGENESB (http://linux1.softberry.com/berry. phtml?topic=fgenesb&group=programs&subgroup= gfindb) (data not shown). Features of genome rearrangement breakpoints. Genome rearrangements ... 


PLoS Pathog
2010 6(4): e1000845. doi:10.1371/journal.ppat.1000845

A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence

Nandi et al.,
1 Genome Institute of Singapore, Singapore, Republic of Singapore, 2 Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore

... Procedures) Act 1986. Genome Annotations and Comparative Analysis. Bp genes were predicted using FGENESB [http://linux1.softberry.com/berry.phtml??topic= fgenesb&group=help&subgroup=gfindb (Softberry)]. tRNA genes ... 


Gene.
2010 Dec 1;469(1-2):31-44. Epub 2010 Aug 12

Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens

Krushkal et al.,
Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA

... Operon prediction The operon organization of the G. sulfurreducens genome (GenBank accession: AE017180) was predicted using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc; 2003-2008), as described earlier ... 


Methods Mol Biol.
2010, Volume 666, Part 2, 197-218, DOI: 10.1007/978-1-60761-820-1_14

Oral bacterial genome sequencing using the high-throughput Roche Genome Sequencer FLX System

Nicholas C.K. Heng and Jo-Ann L. Stanton
Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand.

... 14.1). 2. Gene prediction can be performed using Web-based tools such as GeneMark.hmm (12) and FGENESB (http:// linux1.softberry.com/berry.phtml?topic= fgenesb&group= programs&subgroup=gfindb) (see Note 27). Another ...


Appl. Environ. Microbiol.
doi:10.1128/AEM.00473-09 2009

Comparative metagenomic analysis of a microbial community from 4000 m at Station ALOHA in the North Pacific Subtropical Gyre

Konstantinos T. Konstantinidis, Jennifer Braff, David M. Karl, and Edward F. DeLong

10 FGENESB pipeline for automatic annotation of bacterial genomes from Softberry 11 (http://www.softberry.com/berry.phtml), using the following parameters and cutoffs: general 12 ...


Plasmid
Volume 61, Issue 1, January 2009, Pages 52-64

Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmids from Exiguobacterium arabatum sp. nov. RFL1109

Jakubauskas et al.,
aInstitute of Biotechnology, Graiciuno g. 8, Vilnius LT-02241, Lithuania bDepartment of Plant Physiology and Microbiology, Faculty of Natural Sciencies, Vilnius University, Ciurlionio g. 21/27, Vilnius LT-03101, Lithuania

... Additionally, the FgenesB program at SoftBerry (http://www.softberry.com) was employed for gene prediction using bacterial generic model. The predicted ORFs and the putative intergenic sequences were further examined by visual inspection. ...


Journal of Bacteriology
January 2009, p. 210-219, Vol. 191, No. 1

Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa

Zegans et al.,
Department of Microbiology and Immunology, Rm. 505 Vail Building, Dartmouth Medical School, Hanover, New Hampshire 03755,1 Department of Surgery, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire 03756

... Transcriptional units were predicted with the help of FGENESB (SoftBerry, Mt. Kisco, NY) set to the generic bacterial genome setting and utilizing default settings. ... Kisco, NY; http://www.softberry. com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). ...


Microbiology
155 (2009), 95-105; DOI 10.1099/mic.0.021873-0

Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28

Carlo Viti, Francesca Decorosi, Annalisa Mini, Enrico Tatti and Luciana Giovannetti
Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Universita` degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy

... nlm.nih.gov). Identification of operons was performed using the FGENESB pattern/Markov chain-based prediction program from Softberry (http://softberry.com/ berry.phtml). RNA extraction and cDNA synthesis. For RNA extraction ...


Journal of Bacteriology
March 2009, p. 1910-1923, Vol. 191, No. 6

Regulation of Cyclic Lipopeptide Biosynthesis in Pseudomonas fluorescens by the ClpP Protease

I. de Bruijn and J. M. Raaijmakers
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

... clpP was identified by sequencing the regions flanking the transposon insertions as described by De Sousa et al. (17). The flanking regions of clpP were sequenced by primer walking, and open reading frames (ORFs) were identified with the Softberry FGENESB program. ...


Applied and Environmental Microbiology
August 2009, p. 5345-5355, Vol. 75, No. 16

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

Konstantinos T. Konstantinidis,1, Jennifer Braff,1 David M. Karl,2 and Edward F. DeLong 1
Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,1 University of Hawaii, Honolulu, Hawaii2

... Fosmid and untrimmed WGS sequences were annotated with the FGENESB pipeline for automatic annotation of bacterial genomes from Softberry, using the following parameters and cutoffs: general parameter file; open reading frame size, 90 nucleotide bases; expectation e ...


Appl Environ Microbiol.
2009 Jul;75(13):4599-615. Epub 2009 May 8.

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms

Goltsman et al.,
University of California-Berkeley, 94720, USA.

... The numerous small contigs were manually curated into 10 scaffolds. Annotation. Gene predictions for Leptospirillum groups II and III were made using a combination of FgenesB (Softberry, Inc.), CRITICA (11), and Glimmer (21). ...


OMICS.
2009 Oct;13(5):439-49.

GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens

Qu Y et al.,
Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA

... Operon organization of the G. sulfur- reducens genome was predicted using a commercial version of the FGENESB software (V. Solovyev and A. Salamov, Soft- berry, Inc, 2003-2008) (Tyson et al., 2004), as described earlier (Krushkal et al., 2007; Mahadevan et al., 2008; Yan ...


BMC Genomics.
2009 Aug 24;10:395.

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528

Studholme et al.,
The Sainsbury Laboratory, Norwich, UK

... pseudomonads Using the FgenesB annotation pipeline (http://www.softberry.com), we identified 6,057 potential Page 7. ... We used Softberry's FgenesB pipeline (http://www. softberry.com) to predict genes encoding rRNAs, tDNAs and proteins. ...


Veterinary Microbiology
Volume 136, Issues 3-4, 12 May 2009, Pages 326-334

Characterisation of an extracellular vibriolysin of the fish pathogen Moritella viscosa

Bjornsdottir et al.,
aInstitute for Experimental Pathology, University of Iceland, Keldur, Vesturlandsvegi, 112 Reykjavik, Iceland bMatis-Prokaria, Gylfaflot 5, 112 Reykjavik, Iceland

... The NCBI Basic Local Alignment Search Tool (BLAST) was used for comparing protein sequences and CD search for detecting conserved domains. Putative open reading frames (ORF) were identified by the SoftBerry FGENESB program. ...


Nucleic Acids Research
doi:10.1093/nar/gkp327

Orphelia: predicting genes in metagenomic sequencing reads

Katharina J. Hoff 1,*, Thomas Lingner 1,2, Peter Meinicke 1 and Maike Tech 1
1Abteilung Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg-August-Universitat Gottingen, Goldschmidtstr. 1, 37077 Gottingen, Germany and 2Center for Genomic Regulation, Comparative Bioinformatics Research Group, Biomedical Research Park, c/Dr. Aiguader 88, 08003 Barcelona, Spain

... Negro (12). Each sample was Sanger sequenced and contains 13 000 reads. The original gene annotation of those reads was created with the commercial program FGENESB (http://www.softberry.com). Note that FGENESB ...


PLoS Genet.
2009 March; 5(3): e1000439.

A Toxin–Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element

Rachel A. F. Wozniak 1,2,3 and Matthew K. Waldor 1,2,3*
1Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America 2Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

... 5? RACE experiments to identify the +1 nucleotide of the mosA transcript (Figure 5B) suggested that the true mosA transcript begins upstream from the original annotation (Figure 5). Promoter and ORF predictions (BProm, FGENESB; http://linux1.softberry.com/berry.phtml) for ...


BMC Microbiology
2009, 9:262 doi:10.1186/1471-2180-9-262

Molecular and biochemical characterization of urease and survival of Yersinia enterocolitica biovar 1A in acidic pH in vitro

Neeru Bhagat and Jugsharan S Virdi
Address: Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi - 110 021, India

... The open reading frames (ORFs) in the compiled ure gene cluster were identified using GeneMark [26], Gene- Mark.hmm [27], FGENESB [28] and the NCBI ORF finder [29] programs... 28. FGENESB [http://www.softberry.com/berry.phtml] ...


BMC Genomics
2009, 10:3doi:10.1186/1471-2164-10-3

Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer

McClain et al.,
1 Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232-2605, USA 2 Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2605, USA

... ORFs in the genomes of H. pylori strains 98-10 and B128 were predicted by FGENESB http:/ / www.softberry.com/ berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb webcite[56], an algorithm based on Markov chain models of coding regions and translation and ...


J. Bacteriol.
2008, doi:10.1128/JB.01558-08

Regulation of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens by the ClpP protease

I. de Bruijn and J. M. Raaijmakers
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

... 13 open reading frames (ORFs) were identified with the Softberry FGENESB program 14 (http://www.softberry.com/berry.phtml). The ...


Microbiology
154 (2008), 2589-2599; DOI 10.1099/mic.0.2008/017244-0

Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation

Carla Risso, Barbara A. Methe, Hila Elifantz, Dawn E. Holmes and Derek R. Lovley
Department of Microbiology, 203N Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA

... Operons, promoters and terminators were predicted using the commercial version of the FGENES-B software package (Softberry Inc.) as previously described (Yan ...


FEMS Microbiology Ecology
2008, Volume 66 Issue 1, Pages 45 - 62

Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331

Mela et al.
Centre for Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands

... The complete nucleotide sequence of pTer331 (40 457 bp) was searched for ORFs using FGENESB (http://www.softberry.com) and by the automated genome ...


Applied and Environmental Microbiology,
December 2008, p. 7152-7162, Vol. 74, No. 23

Proteome-Based Comparative Analyses of Growth Stages Reveal New Cell Cycle-Dependent Functions in the Predatory Bacterium Bdellovibrio bacteriovorus

Mally Dori-Bachash, Bareket Dassa, Shmuel Pietrokovski, and Edouard Jurkevitch
Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel,1 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel

... Operons were predicted with the Softberry fgenesb program using the B. bacteriovorus 100 T genome sequence (http://www.softberry.com/berry.phtml?topic ...


PNAS
November 11, 2008 vol. 105 no. 45 17516-17521

Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility

Grzymski et al.
aDivision of Earth and Ecosystem Sciences, Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512; bCollege of Marine and Earth Studies, University of Delaware, Lewes, DE 19958;

... We integrated several annotation tools, including BLAST (46), FgenesB (Softberry) for gene calling and COG assignment, PRIAM (47), and a custom Pfam database ...


Microbiology and Molecular Biology Reviews,
December 2008, p. 557-578, Vol. 72, No. 4

A Bioinformatician's Guide to Metagenomics

Victor Kunin, Alex Copeland, Alla Lapidus, Konstantinos Mavromatis, and Philip Hugenholtz
Microbial Ecology Program,1 Quality Assurance Department,2 Microbial Genomics Department,3 Genome Biology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California4

.. of the same or related organisms, can enhance the quality of the predicted genes for some of those programs (eg, fgenesB [http://www.softberry.com]), while ...


Biochem. J.
(2008) Immediate Publication, doi:10.1042/BJ20081488

Characterization of the phenylurea hydrolases A and B: founding members of a novel amidohydrolase subgroup

Khurana et al.
Division of Entomology, CSIRO, Canberra, ACT 2601, Australia.

... Genomic and phylogenetic analysis. FGENESB (http://www.softberry.com) was used to detect open reading frames (ORFs), which were then manually confirmed. ...


J Bacteriol.
2008 May;190(9):3362-73. Epub 2008 Feb 29.

The sim operon facilitates the transport and metabolism of sucrose isomers in Lactobacillus casei ATCC 334

Thompson J, Jakubovics N, Abraham B, Hess S, Pikis A.
Microbial Biochemistry and Genetics Unit, NIDCR, National Institutes of Health, Bldg. 30, Rm. 325, Convent Dr. MSC-4350, Bethesda, MD 20892, USA

... The structure of operons was predicted by automated genome annotation using the fgenesB module of the MolQuest software (Softberry Inc.). ...


BMC Genomics
2008, 9:471 doi:10.1186/1471-2164-9-471

Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function

Hoa T Tran, Julia Krushka, Frances M Antommattei, Derek R Lovley and Robert M Weis
1Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA, 2Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA, 3Sharon Woods Technical Center, Procter and Gamble, Cincinnati, OH 45040, USA and 4Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

... The organization of che gene operons in the Geobacter sp. was predicted with FGENESB (Softberry Inc., http:// www.softberry.com). FGENESB identifies protein-coding genes with Markov chain models of coding regions and translation start and termination sites, and annotates them with information from public databases. The sequence parameters (coding content, oligonucleotide composition, and gene length distribution) were estimated in FGENESB for each genome separately through an iterative procedure with the minimum ORF length set to 100 nt. ...


Expert Opinion on Drug Discovery
August 2008, Vol. 3, No. 8, Pages 903-929 (doi:10.1517/17460441.3.8.903)

Systems biology of cyanobacterial secondary metabolite production and its role in drug discovery

Nishikant V Wase & Phillip C Wright
The University of Sheffield, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, Mappin St., Sheffield, S1 3JD, UK +44 0 114 2227577; +44 0 114 2227501

... This can be done through software packages such as GLIMMER [61] and GENEMARK [62], and a list of software packages found on Softberry [63], including fgenesB ...


Journal of Microbiological Methods
Volume 75, Issue 3, December 2008, Pages 515-522

A procedure for the metagenomics exploration of disease-suppressive soils

J.D. van Elsas, A.J. Speksnijder and L.S. van Overbeek
aDepartment of Microbial Ecology, Centre for Ecological and Evolutionary Studies University of Groningen, Kerklaan 30, 9750AA Haren, The Netherlands bGGD Amsterdam, Nieuwe Amstergracht 100, 1018WT Amsterdam, The Netherlands cPlant Research International BV, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

... Sequence assemblies were screened with the FgenesB programme (Softberry Inc.) and the PKS-NRPS search tool (http://www.nii.res.in/nrps-pks.html). ...


Trends in Genetics
Volume 24, Issue 3, March 2008, Pages 142-149

Bioinformatics challenges of new sequencing technology

Mihai Pop and Steven L. Salzberg
Center for Bioinformatics and Computational Biology, University of Maryland, MD 20742, USA

.. They compared fgenesb (www.softberry.com) with a pipeline combining CRITICA [43] and Glimmer [44], using three datasets of varied complexity constructed by ..


Foodborne Pathogens and Disease.
August 1, 2008, 5(4): 387-398. doi:10.1089/fpd.2008.0113.

Genomic Evidence for Interspecies Acquisition of Chromosomal DNA from Campylobacter jejuni by Campylobacter coli Strains of a Turkey-Associated Clonal Group (Cluster II)

Kamfai Chan, Driss Elhanafi, Sophia KathariouBowler et al.
Department of Food Science, North Carolina State University, Raleigh, North Carolina.

... Assembled DNA sequences were submitted to the web-based FgenesB program (Softberry Inc., http:==www.softberry.com) to identify open reading frames (ORFs). ...


Applied and Environmental Microbiology
July 2008, p. 4149-4163, Vol. 74, No. 13 doi:10.1128/AEM.02371-07

In Silico and In Vivo Evaluation of Bacteriophage fEF24C, a Candidate for Treatment of Enterococcus faecalis Infections

Jumpei Uchiyama, Mohammad Rashel, Iyo Takemura, Hiroshi Wakiguchi, and Shigenobu Matsuzaki
Departments of Pediatrics,1 Microbiology and Infection, Kochi Medical School, Oko-cho, Nankoku City, Kochi 783-8505, Japan2

... first predicted by the following gene predication tools: GeneMark VIORIN (http://opal.biology.gatech.edu/GeneMark/) (3), FGENESB (http://www.softberry.com/ ...


Journal of Bacteriology
May 2008, p. 3646-3657, Vol. 190, No. 10

Regulation of Gene Expression in a Mixed-Genus Community: Stabilized Arginine Biosynthesis in Streptococcus gordonii by Coaggregation with Actinomyces naeslundii

Nicholas S. Jakubovics,1 Steven R. Gill,2,4 Stacey E. Iobst,4 M. M. Vickerman,2,3 and Paul E. Kolenbrander
National Institute of Dental and Craniofacial Research, National Institutes of Health, Building 30, Room 310, Bethesda, Maryland 20892,1 Department of Oral Biology,2 Department of Periodontics and Endodontics, University at Buffalo School of Dentistry, Buffalo, New York,3 Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 208504

... gordonii genome sequence were detected using the BProm and FindTerm modules of the fgenesB gene prediction program in Molquest software (Softberry Inc., Mount ...


J. Bacteriol.
July 2008, p. 4859-4864, Vol. 190, No. 14 doi:10.1128/JB.02022-07

Genes and Enzymes of Azetidine-2-Carboxylate Metabolism: Detoxification and Assimilation of an Antibiotic

Carol Gross, Roderick Felsheim, and Lawrence P. Wackett
Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, 140 Gortner Laboratory, University of Minnesota, St. Paul, MN 55108

... open reading frames were found in the seven kilobase fragment using BlastX on the 21 NCBI server and the Softberry program FGENESB. ...


Environmental Microbiology
Volume 10 Issue 1 Page 200-207, January 2008

Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses

Gene W. Tyson, Jillian F. Banfield
Departments of 1Environmental Science, Policy and Management and 2Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.

... Annotations were performed using fgenesb (Softberry) and were subsequently manually refined using artemis (Rutherford et al., 2000). ...


Antimicrob. Agents Chemother.
doi:10.1128/AAC.01643-07

Whole genome pyrosequencing of an epidemic multidrug resistant Acinetobacter baumannii of the European clone II

Iacono et al.,
National Research Council, Segrate, 20090 Milan; Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanita`; Department of Biology, University Roma Tre, Rome, Italy; Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

... Coding genes were identified by crossing predictions from FGENESB package (24) 19 (http://www.softberry.com/), GeneMark (7) and GLIMMER (14). ...


Applied and Environmental Microbiology,
February 2008, p. 774-782, Vol. 74, No. 3

Enzymic Approach to Eurythermalism of Alvinella pompejana and Its Episymbionts

Charles K. Lee, S. Craig Cary, Alison E. Murray, and Roy M. Daniel
Department of Biological Sciences, University of Waikato, Hamilton, New Zealand, College of Marine and Earth Studies, University of Delaware, Lewes, Delaware, Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada

... The metagenomic sequences were annotated with a custom annotation pipeline based on the FGenesB package (SoftBerry Inc., Mount Kisco, NY), blastX, and PRIAM ...


OMICS: A Journal of Integrative Biology
March 1, 2008, 12(1): 33-59. doi:10.1089/omi.2007.0043.

Characterizing Regulation of Metabolism in Geobacter sulfurreducens through Genome-Wide Expression Data and Sequence Analysis

Radhakrishnan Mahadevan et al.,
Department of Microbiology, University of Massachusetts, Amherst, Massachusetts. Department of Preventive Medicine, University of Tennessee Health Science Center, 66 Memphis, Tennessee.

... Operons were predicted using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc., 2003-2005) that ...


FEMS Microbiology Ecology
Volume 65 Issue 2, Pages 238 - 250 doi:10.1111/j.1574-6941.2008.00436.x

Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid

Johan H.J. Leveau, Saskia Gerards
Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands

... FGENESB (SoftBerry, Mount Kisco, NY) and GenDB (Meyer et al., 2003) were used to annotate the consensus DNA of the largest contig. Results. ...


PLoS ONE
2008; 3(4): e1862.

The Airborne Metagenome in an Indoor Urban Environment

Susannah G. Tringe et al.,
1Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America

... Protein prediction. All assembled contigs as well as all singlet reads that failed to assemble were annotated using Fgenesb (www.softberry.com). ...


Infection and Immunity
April 2008, p. 1485-1497, Vol. 76, No. 4

Further Characterization of Vibrio vulnificus Rugose Variants and Identification of a Capsular and Rugose Exopolysaccharide Gene Cluster

Brenda L. Grau et al.,
Department of Biological Sciences,1 Socolofsky Microscopy Center,2 Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana3

... Using the web-based FGENESB: Bacterial Operon and Gene Prediction algorithm (http://www.softberry.com/cgi-bin/programs/gfindb/fgenesb.pl), two operons were ...


Molecular Systems Biology
4 Article number: 198 doi:10.1038/msb.2008.35

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Kunin et al.,
Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

... Genes were predicted on vector and quality-trimmed reads with fgenesb (http://www. softberry.com/) using a generic bacterial model, resulting in an average of ...


Journal of Bacteriology,
April 2008, p. 2777-2789, Vol. 190, No. 8

Massetolide A Biosynthesis in Pseudomonas fluorescens

I. de Bruijn,1 M. J. D. de Kock,1 P. de Waard,2 T. A. van Beek,3 and J. M. Raaijmakers1*
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands,1 Wageningen NMR Centre, Wageningen University, Wageningen, The Netherlands,2 Natural Products Chemistry Group, Laboratory of Organic Chemistry, Wageningen University, Wageningen, The Netherlands3

... Bacterial operons and genes were subsequently predicted by the Softberry FGENESB program (Softberry, Inc., Mount Kisco, NY), and the identified open reading ...


FEMS Microbiology Ecology
2008 doi:10.1111/j.1574-6941.2008.00472.x

Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331

Francesca Mela et. al.,
1Centre for Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands; 2Department of Microbial Ecology, University of Groningen, Haren, The Netherlands; and 3Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, USA

... The complete nucleotide sequence of pTer331 (40 457 bp) was searched for ORFs using FGENESB (http://www.softberry.com) and by the automated genome ...


Microbiology
154 (2008), 1422-1435; DOI 10.1099/mic.0.2007/014365-0

Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes

Dawn E. Holmes et. al.,
Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

... FGENESB, BPROM and FindTerm programs, available through SoftBerry (www.softberry. com), were used for operon and gene predictions. RESULTS. ...


Infection and Immunity,
September 2007, p. 4482-4489, Vol. 75, No. 9

Genetic Basis for the New Pneumococcal Serotype, 6C

In Ho Park, Saeyoung Park, Susan K. Hollingshead, and Moon H. Nahm
Departments of Pathology,1 Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 614, Birmingham, Alabama 35294

... and genes, promoters, and transcription terminators in the capsule gene locus were identified using fgenesB, BPROM, and FindTerm (Softberry Inc.), which are ...


Microbiology
153 (2007), 3478-3498; DOI 10.1099/mic.0.2007/008250-0

Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5'-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes

Birte Meyer and Jan Kueve
Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany

... promoters, termination sites and gene arrangement in operons was performed using the web versions FGENESB, BPROM and BTERM of the Softberry program package ...


Microbiology
153 (2007), 2026-2044; DOI 10.1099/mic.0.2006/003152-0

Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway

Birte Meyer and Jan Kueve
Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany

... promoters, termination sites and operons in genome data were performed using the web versions FGENESB, BPROM and BTERM of the Softberry program package ...


Journal of Biotechnology
Volume 131, Issue 4, 30 September 2007, Pages 371-378

Characterization of the unique organization and co-regulation of a gene cluster required for phenol and benzene catabolism in Pseudomonas sp. M1

Pedro M. Santos and Isabel Sa'-Correia
BB, Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Te'cnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal

... This 9 kb chromosomal DNA sequence was analyzed using the gene prediction program FGENESB from the Softberry online package (http://www.softberry.com/), the ...


Applied and Environmental Microbiology
August 2007, p. 4984-4995, Vol. 73, No. 15

Transposon Insertion Reveals pRM, a Plasmid of Rickettsia monacensis

Gerald D. Baldridge, Nicole Y. Burkhardt, Roderick F. Felsheim, Timothy J. Kurtti, and Ulrike G. Munderloh
Department of Entomology, University of Minnesota, St. Paul, Minnesota 55108

... encoded by other bacteria (Table 2). Four pRM genes (pRM17 to pRM20) were identified as members of an operon by the FGENESB program (SoftBerry, Inc.), while ...


European Journal of Plant Pathology
Volume 119, Number 3 / November 2007 p. 279-300

The magic and menace of metagenomics: prospects for the study of plant growth-promoting rhizobacteria

Johan H. J. Leveau
Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands

... al. 2003), Artemis (Rutherford et al. 2000), Glimmer (Delcher et al. 1999), and FGenesB pipeline (www.softberry.com). These programmes ...


Functional & Integrative Genomics
Volume 7, Number 3 / July 2007 p. 229-255

Genome-wide expression profiling in Geobacter sulfurreducens : identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant

Julia Krushkal et.al.,
Department of Preventive Medicine, University of Tennessee Health Science Center, 66 N. Pauline Ste. 633, Memphis, TN 38163, USA

... 2003) using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc; 2003-2006). ...


Applied and Environmental Microbiology
July 2007, p. 4417-4424, Vol. 73, No. 14

Comparative Sequence Analysis of Plasmids from Lactobacillus delbrueckii and Construction of a Shuttle Cloning Vector

Ju-Hoon Lee, Jamie S. Halgerson, Jeong-Hwan Kim, and Daniel J. O'Sullivan
Department of Food Science and Nutrition and Center for Microbial and Plant Genomics, University of Minnesota, Cargill Building for Microbial and Plant Genomics, 1500 Gortner Ave., St. Paul, Minnesota 55108

... Prediction of open reading frames (ORFs) was conducted with GeneMark (4) and the FgenesB (Softberry, Inc., Mount Kisco, NY) programs. ...


Plasmid
Volume 58, Issue 3, November 2007, Pages 240-248

The polyhydroxyalkanoate genes of a stress resistant Antarctic Pseudomonas are situated within a genomic island

Nicolas D. Ayub, M. Julia Pettinari, Beatriz S. Mendez and Nancy I. Lopez
Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina

... and bacterial operons were predicted by using GeneMark.hmm for Prokaryotes Version 2.4 (Lukashin and Borodovsky, 1998) and FGENESB (http://www.softberry.com). ...


Applied and Environmental Microbiology,
July 2007, p. 4226-4233, Vol. 73, No. 13

Possible Origins of CTnBST, a Conjugative Transposon Found Recently in a Human Colonic Bacteroides Strain

David J. Schlesinger, Nadja B. Shoemaker, and Abigail A. Salyers
Department of Microbiology, University of Illinois, Urbana, Illinois 61801

... reading frames (ORFs) were identified by using two Web-based ORF finding programs, GeneMark (2) and FGENESB: Bacterial Operon and Gene Prediction (Softberry Inc ...


PROTEOMICS
Volume 7, Issue 12 , Pages 2047 - 2058, 2007

Qualitative and comparative proteomic analysis of Xanthomonas campestris pv. campestris 17

Wei-Jen Chung et al.,
Sequencing Core, Genome Research Center, National Yang-Ming University, Taipei, Taiwan

... Operon predic- tion was carried out using FGENESB from Softberry, which predicts genes and operons as well as functional RNA (http://www.softberry.com/berry ...


Nature Biotechnology
25, 447 - 453 (01 Apr 2007)

Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338

Oliynyk et al.,
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

...sequence. Genome analysis and annotation. CDSs were predicted and annotated using the program fgenesB (http://www.softberry.com/), trained ab initio, and manually curated using Artemis (version 8) and a set of in-house PERL scripts....


Environmental Microbiology
Volume 9 Issue 4 Page 846-858, April 2007

Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla

Jay McCarren and Edward F. DeLong**
Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

... Sequences were assembled with Sequencher v4.5 (Gene Codes, Ann Arbor, MI, USA) and annotated with both FGENESB (Softberry, Mount Kisco, NY, USA) and Artemis ...


BMC Evolutionary Biology
2007, 7:79 (18 May 2007)

Evolution of rhodopsin ion pumps in haloarchaea

Sharma AK et al.,,
1Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
2Unidad de Microbiologia, Centro de Biologia Molecular y Celular, Universidad Miguel Hernandez, Campus de San Juan, 03550 San Juan, Alicante, Spain

and open reading frames (ORFs) were identified using the fgenesB option under operon and gene finding in bacteria at [66] with Halobacterium sp.


PNAS
| March 27, 2007 | vol. 104 | no. 13 | 5590-5595

Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host

A. Martinez*, A. S. Bradley, J. R. Waldbauer, R. E. Summons, and E. F. DeLong*,
*Department of Civil and Environmental Engineering, Division of Biological Engineering, and Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and Joint Program in Chemical Oceanography, Woods Hole Oceanographic Institution and Massachusetts Institute of Technology, Cambridge, MA 02139

... complete DNA sequence was assembled by using Sequencher version 4.5 (Gene Codes Corporation, Ann Arbor, MI) and annotated with FGENESB (Softberry, Mount Kisco ...


Nature Methods
- 4, 495 - 500 (2007)

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Konstantinos Mavromatis et al.,
Department of Energy Joint Genome Institute (DOE-JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA.

...We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER)....
... fgenesb: http://sun1.softberry.com/berry.phtml?topic= fgenesb&group=programs&subgroup=gfindb; FAMeS: http://fames.jgi-psf.org...


Nature Biotechnology
24, 1263 - 1269 (2006) Published online: 24 September 2006; | doi:10.1038/nbt1247

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Hector Garcia Martin et al.,
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.

... Over 30,000 coding sequences were predicted in each Phrap assembly using ab initio gene predictions (fgenesb, http://www.softberry.com/). ...


BIOINFORMATICS
Vol. 22 no. 14 2006, pages e359 - e367 doi:10.1093/bioinformatics/btl217

An experimental metagenome data management and analysis system

Victor M. Markowitz et al.,
1Biological Data Management and Technology Center, Lawrence Berkeley National Lab, USA,
2Genome Biology Program, Joint Genome Institute, USA and 3Microbial Ecology Program, Joint Genome Institute, USA

... protein-coding genes (CDSs) are predicted on scaffolds and/or so called shrapnel sequences (single reads that are not incorporated into scaffolds) using microbial gene finders, such as Glimmer (Delcher et al., 1999) or Fgenesb (Soft- Berry, 2006)...


Journal of Bacteriology
December 2006, p. 8283-8293, Vol. 188, No. 23

Pip, a Novel Activator of Phenazine Biosynthesis in Pseudomonas chlororaphis PCL1391

Genevieve Girard et al.,
Leiden University, Institute of Biology, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands,
Leiden University, Leiden Institute of Chemistry, Department of Molecular Genetics, P.O. Box 9502, 2300 RA Leiden, The Netherlands

... gov/BLAST). A search for bacterial promoters and terminators was done using Softberry (http://www.softberry.com). Alignments of ...


Nature Biotechnology ,
24, 1263 - 1269 (01 Oct 2006) Research

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Martin et al.,
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA

..coding sequences were predicted in each Phrap assembly using ab initio gene predictions (fgenesb, http://www.softberry.com/). The genomic fragments were binned (classified) using a combination of read depth, % GC content,...


PNAS ,
August 22, 2006 vol. 103 no. 34 12897-12902

Deletion of TolC orthologs in Francisella tularensis identifies roles in multidrug resistance and virulence

Gil et al.,
Center for Infectious Diseases, Stony Brook University, Stony Brook, NY 11794-5120

... 42). The locations of promoters and operons were investigated by using the FGENESB and BPROM programs available from Softberry (Mt. Kisco, NY). ...


Applied and Environmental Microbiology ,
May 2006, p. 3154-3160, Vol. 72, No. 5

Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida

Susana Campoy,1, Jesus Aranda,2, Gerard Alvarez,2 Jordi Barbe,1,2 and Montserrat Llagostera1,2*
Centre de Recerca en Sanitat Animal (CReSA),1 Departament de Genetica i Microbiologia, Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain2

... Open reading frames (ORFs) were identified using Glimmer 2.02 (http://nbc11.biologie. uni-kl.de/glimmer2.02) (8) and FGENESB (http://softberry.com) (34) for ...


Journal of Bacteriology ,
July 2006, p. 5228-5239, Vol. 188, No. 14

Global Transcriptome Analysis of Tropheryma whipplei in Response to Temperature Stresses

Nicolas Crapoulet,1 Pascal Barbry,2 Didier Raoult,1 and Patricia Renesto1*
Unite des Rickettsies, UMR 6020 CNRS, IFR48, Faculte de Medecine, 27, Boulevard Jean Moulin, Marseille, France,1 Institut de Pharmacologie Moleculaire et Cellulaire, UMR 6097 CNRS/UNSA, Sophia Antipolis, France2

... genome. Their coexpression thus confirms the bioinformatic dnaK operon prediction (FGENESB software; Softberry Inc., Mount Kisco, NY). ...


Microbiology ,
152 (2006), 1951-1968

Two novel conjugative plasmids from a single strain of Sulfolobus

Gael Erauso1,2, Kenneth M. Stedman3,4, Harmen J. G. van de Werken1, Wolfram Zillig3, and John van der Oost1
1 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands

.. Identification of putative genes and operons was performed using the FGENESB pattern/Markov chain-based prediction program from Softberry (http://softberry.com ...


Molecular Microbiology ,
(2006) 61 (4), 960-977

Metagenomic DNA fragments that affect Escherichia coli mutational pathways

Yang, Hanjing, To, Kam H., Aguila, Sharon J. & Miller, Jeffrey H.
Department of Microbiology, Immunology and Molecular Genetics, and the Molecular Biology Institute, 1602 Molecular Sciences Building, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095, USA

.. The ORFs on each clone were annotated by a bacterial operon and gene prediction program fgenesb ( http:/ / www.softberry.com ) and by comparison with known ...


Applied and Environmental Microbiology ,
May 2006, p. 3154-3160, Vol. 72, No. 5

Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida

Susana Campoy,1, Jesus Aranda,2, Gerard Alvarez,2 Jordi Barbe,1,2 and Montserrat Llagostera1,2*
Centre de Recerca en Sanitat Animal (CReSA),1 Departament de Genetica i Microbiologia, Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain2

... Open reading frames (ORFs) were identified using Glimmer 2.02 (http://nbc11.biologie. uni-kl.de/glimmer2.02) (8) and FGENESB (http://softberry.com) (34) for ...


Applied and Environmental Microbiology,
February 2006, p. 1532-1541, Vol. 72, No. 2

Comparative Genomics of DNA Fragments from Six Antarctic Marine Planktonic Bacteria

Joseph J. Grzymski,1 Brandon J. Carter,1 Edward F. DeLong,2 Robert A. Feldman,3, Amir Ghadiri,3 and Alison E. Murray1
Desert Research Institute, 2215 Raggio Parkway, Reno, Nevada 89512,1 Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139,2 Amersham Biosciences, 928 E. Argues Avenue, Sunnyvale, California 940863

... Two gene finding programs, FgenesB (Softberry Inc.) and GLIMMER (TIGR), identified open reading frames (ORFs). The results from ...


Nature
439, 847-850 (16 February 2006)

Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea

Niels-Ulrik Frigaard, Asuncion Martinez, Tracy J. Mincer & Edward F. DeLong
Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Building 48, 15 Vassar Street, Cambridge, Massachusetts 02139, USA.

... Subcloning kit (Invitrogen) combined with sequence assembly with Sequencher v. 4.5 (Gene Codes Corporation) and annotation with FGENESB (Softberry) and Artemis ...


FEMS Microbiology Letters,
2006 257 (2), 177-181.

Isolation of a novel plasmid, pNi15, from Enterobacter sp. Ni15 containing a nickel resistance gene

Young-Keun Lee et al.,
Radiation Application Research Division, ARTI, Korea Atomic Energy Research Institute, Sinjeong-Dong, Jeongeup, Korea

... bp in size and it contains six ORFs (four in a plus strand and two in a minus strand) which were analyzed using the FGENESB program at http://www.softberry.com ...


PLoS Biol
2006 4(4): e95

Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota

Steven J. Hallam et al.,
Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America,

... Fosmid sequences were annotated using the FGENESB pipeline for automatic annotation of bacterialgenomes from Softberry (http:/ / www.softberry.com/ berry.phtml ...


Applied and Environmental Microbiology
December 2005, p. 8506-8513, Vol. 71, No. 12

Sequence and Expression Analyses of Cytophaga-Like Hydrolases in a Western Arctic Metagenomic Library and the Sargasso Sea

Matthew T. Cottrell, Liying Yu, and David L. Kirchman
University of Delaware, College of Marine Studies, Lewes, Delaware 19958

... obtained from the Welcome Trust Sanger Institute (http://www.sanger.ac.uk/Software/ Artemis/) and using the FGENESB website (http://www.softberry.ru/) (Softberry ...


Infection and Immunity
August 2005, p. 4982-4992, Vol. 73, No. 8

Characterization of the cciIR Quorum-Sensing System in Burkholderia cenocepacia

Rebecca J. Malott,1 Adam Baldwin,2 Eshwar Mahenthiralingam,2 and Pamela A. Sokol
Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, Calgary, Alberta, Canada T2N 4N1,1 Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, Wales2

... Cell-Cell Commun. Bacteria, 2004). The promoter regions for cciI and cciR were predicted in silico using SoftBerry BPROM (http://www.softberry.com). ...


Science,
2005 308 (5721) 554-557
Science Supporting Online Material

Comparative Metagenomics of Microbial Communities

Susannah Green Tringe, Christian von Mering, Arthur Kobayashi, Asaf A. Salamov, Kevin Chen, Hwai W. Chang, Mircea Podar, Jay M. Short, Eric J. Mathur, John C. Detter, Peer Bork, Philip Hugenholtz, Edward M. Rubin

... Functional annotation All genomic sequences from soil, whale falls and acid mine drainage were analyzed by the program FGENESB from Softberry, which predicts...


Nature
428, 37-43 (4 March 2004)

Community structure and metabolism through reconstruction of microbial genomes from the environment

Gene W. Tyson1, Jarrod Chapman3,4, Philip Hugenholtz1, Eric E. Allen1, Rachna J. Ram1, Paul M. Richardson4, Victor V. Solovyev4, Edward M. Rubin4, Daniel S. Rokhsar3,4 and Jillian F. Banfield1,2
1. Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
2. Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
3. Department of Physics, University of California, Berkeley, California 94720, USA
4. Joint Genome Institute, Walnut Creek, California 94598, USA

...To identify protein and RNA genes in genomic sequences from an environmental sample we applied the Fgenesb_annotator pipeline developed by Softberry Inc (http://www.softberry.com/berry.phtml?topic=gfindb) which provides completely automatic comprehensive annotation of bacterial sequences...


Appl Environ Microbiol.
2004 April; 70(4): 2332-2341

Oxygen-Controlled Bacterial Growth in the Sponge Suberites domuncula: toward a Molecular Understanding of the Symbiotic Relationships between Sponge and Bacteria

Werner E. G. Muller,* Vladislav A. Grebenjuk, Narsinh L. Thakur, Archana N. Thakur, Renato Batel, Anatoli Krasko, Isabel M. Muller, and Hans J. Breter Institut fur Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Universitat Mainz, D-55099 Mainz, Germany
*Corresponding author. Mailing address: Institut fur Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Universitat Mainz, Duesbergweg 6, 55099 Mainz, Germany. Phone: 6131-3925910. Fax: 6131-3925243. E-mail: wmueller@mail.uni-mainz.de

... For genes and potential promoter prediction, we used the FGENESB-Pattern/Markov chain-based bacterial operon and gene prediction program from the SoftBerry ...


Molecular Microbiology
Volume 52 Issue 6 Page 1579 - June 2004 doi:10.1111/j.1365-2958.2004.04086.x

Gene conversion: a mechanism for generation of heterogeneity in the tprK gene of Treponema pallidum during infection

Arturo Centurion-Lara*, et al
Affiliations: Departments of Medicine and Pathobiology, University of Washington, Harborview Medical Center, Box 359779, 325 Ninth Ave., Seattle, WA 98104, USA.

... Using the fgenesb program, which identifies putative operons and genes in microbial genomes (Softberry; http:/ / www.softberry.com/ berry.phtml ), the tprK ORF ...


Journal of Theoretical Biology
230 (2004) 133-144

Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae

Bin Yana, Barbara A. Methe´ b, Derek R. Lovleyc, Julia Krushkala,*
aDepartment of Preventive Medicine, Center of Genomics and Bioinformatics, University of Tennesee Health Science Center, 66 N. Pauline St., Ste. 633, Memphis, TN 38163, USA
bThe Institute for Genomic Research, Rockville, MD, USA
cDepartment of Microbiology, Morrill Science Center IV North, University of Massachusetts, 639 North Pleasant Str., Amherst, MA 01003, USA

... the conserved nature of the operons 2 . Operons in Geobacter sulfurreducens were predicted ab initio by the public version of program FGENESB (V. Solovyev and V ...


Molecular Microbiology
Volume 52 Issue 6 Page 1579 -1596 June 2004 doi:10.1111/j.1365-2958.2004.04086.x

Gene conversion: a mechanism for generation of heterogeneity in the tprK gene of Treponema pallidum during infection

Arturo Centurion-Lara*, Rebecca E. LaFond, Karin Hevner, Charmie Godornes, Barbara J. Molini, Wesley C. Van Voorhis and Sheila A. Lukehart

... Using the fgenesb program, which identifies putative operons and genes in microbial genomes (Softberry; http:/ / www.softberry.com/ berry.phtml ), the tprK ORF ...

Plasmid
Volume 52, Issue 2, September 2004, Pages 131-138

Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum

Anders Clausen a, 1, 2, Marie Just Mikkelsen a, 2, Imke Schroder b and Birgitte K. Ahring
a Biocentrum-DTU, Building 227, DK-2800, Lyngby, Denmark b Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA, USA

... 1913), and orf61 (1897-2223) are predicted to represent genes, when a FGENESB gene prediction is run using Bacillus subtilis parameters at www.softberry.com. ...



Environmental Microbiology,
September 2004, vol. 6, no. 9, pp. 903-910(8) DOI: 10.1111/j.1462-2920.2004.00676.x

Different SAR86 subgroups harbour divergent proteorhodopsins

Gazalah Sabehi1; Oded Beja1; Marcelino T. Suzuki2; Christina M. Preston3; Edward F. DeLong4 Affiliations: 1: Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel. 2: Chesapeake Biological Laboratory, University of Maryland Center for Environmental Sciences, Solomons, MD 20688, USA. 3: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA. 4: Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

... program. FGENESB (Softberry), and the annotation was subsequently refined and curated manually using ARTEMIS (Sanger Center). Fig. ...


Proc Natl Acad Sci U S A.
2003 October 28; 100(22): 12830-12835. doi: 10.1073/pnas.2133554100. Published online 2003 October 17.
Evolution

Proteorhodopsin genes are distributed among divergent marine bacterial taxa

Jose R. de la Torre, Lynne M. Christianson, Oded Beja, Marcelino T. Suzuki, David M. Karl, John Heidelberg,** and Edward F. DeLong
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039; §Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Chesapeake Biological Laboratory, University of Maryland, Solomons, MD 20688; Department of Oceanography, University of Hawaii, Manoa, HI 96822; and **Institute for Genomic Research, Rockville, MD 20850 Edited by Sallie W. Chisholm, Massachusetts Institute of Technology, Cambridge, MA, and approved August 21, 2003, (received for review 2003 June 10)
Present address: Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195.
To whom correspondence should be addressed. E-mail: delong@mbari.org.

... Analysis of the potential genes and protein-coding regions was performed by using a combination of the BLAST (11), GLIMMER 2.02 (TIGR) (12, 13), FGENESB (Softberry, Mount Kisco, NY), and ARTEMIS (Sanger Center, Cambridge University, U.K.) (14) software packages.


BPROM

FEMS microbiology letters
2014, 353(2), 98-105. DOI:10.1111/1574-6968.12411

The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum f. sp. lycopersici

Xu, J. et al.,
1 Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture/Jiangsu Academy of Agricultural Sciences, Nanjing, China 2 Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA

... Promoter prediction was conducted using the web-based software bprom in the Softberry package (Solovyev & Salamov, 2011). Illumina sequencing was used to determine the pqq gene cluster of P. kilonensis JX22, as described previously (Jalan et al., 2011). ...


Microbiology
2014, 160(Pt 1), 102-112. DOI:10.1099/mic.0.070664-0

OxyR-dependent expression of a novel glutathione S-transferase (Abgst01) gene in Acinetobacter baumannii DS002 and its role in biotransformation of organophosphate insecticides

Longkumer, T., Parthasarathy, S., Vemuri, S. G., Siddavattam, D.
Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India

... ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) was used to predict ORFs and bprom software (http://linux1.softberry.com/berry.phtml?topic=bprom&group= programs&subgroup=gfindb) was used for promoter predictions. ...


ACS synthetic biology
April 4, 2014 DOI:10.1021/sb4001189

A synthetic anhydrotetracycline-controllable gene expression system in Ralstonia eutropha H16

Li H., Liao J. C.
†Department of Chemical and Biomolecular Engineering, ‡The Molecular Biology Institute, §Department of Chemistry & Biochemistry, Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095, United States

... Using the bioinformatic tool (BPROM, Softberry), we identified the putative ?10 and ?35 elements of the P rrsC and the transcriptional start site (Figure 1A). There are two different tetO operators (tetO1 and tetO2) that can both be recognized by the tetR repressor.(13) We took a ...


Annals of Microbiology
2014, 64(2), 809-814. DOI: 10.1007/s13213-013-0717-7

Characterization of the cryptic plasmid pWCZ from Lactobacillus paracasei WCZ isolated from silage

Fu, Y., Zhai, Z., An, H., Hao, Y.
1. Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China

... DNASTAR software package was employed to detect direct and inverted repeats. Putative promoter and terminator predictions were analyzed with BPROM and FindTerm, respectively (http://linux1.softberry.com/berry.phtml). ...


International journal of food microbiology
2014, 177, 89-97. DOI: 10.1016/j.ijfoodmicro.2014.02.011

Response of S. thermophilus LMD-9 to bacitracin: Involvement of a BceRS/AB-like module and of the rhamnose–glucose polysaccharide synthesis pathway

Thevenard B. et al.,
a INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France b AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France

... The presence of putative promoters, terminators, and operons was evaluated using BPROM (http://linux1.softberry.com/berry.phtml), BDGP (http://www.fruitfly.org/seq_tools/promoter.html), FINDTERM (http://linux1.softberry.com/berry.phtml), TranstermHP (http://transterm.cbcb ...


Microbiology
2014, 160(Pt 2), 406-417. DOI: 10.1099/mic.0.074773-0

Exopolyphosphatase of Pseudomonas aeruginosa is essential for the production of virulence factors, and its expression is controlled by NtrC and PhoB acting at two interspaced promoters

Gallarato L. A. et al.,
1Departamento de Biologia Molecular, FCEFQyN, Universidad Nacional de Rio Cuarto, Ruta 36-Km 601, (5800) Rio Cuarto, Cordoba, Argentina 2Departamento de Ingenieria Celular y Biocatalisis, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos 62210, Mexico

... 1999). prodoric was used to determine the integration host factor (IHF) consensus (Munch et al., 2003). The bprom tool from the SoftBerry server (http://linux1.softberry. com) was used to identify ? 70 -dependent promoters. NtrC ...


PloS one
2014, 9(2), e90087. DOI: 10.1371/journal.pone.0090087

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

Sierra-Garcia I. N. et al.,
Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil Laboratory of Genomics and Expression, University of Campinas - UNICAMP, Campinas, Brazil

... several tools available for gene prediction in prokaryotes through heuristic approaches: Metagene [14] http://metagene.cb.ku-tokyo.ac.jp/) and MetaGeneMark [15] designed for metagenomic sequences, GLIMMER 3.02 [16], [17] and FGENESB (http://linux1.softberry.com/berry ... ...Putative ribosomal binding sites were identified using RBSFINDER [22], and the presence of bacterial promoters and transfer RNA genes was predicted using the programs BPROM (http://linux1.softberry.com/berry.phtml) and tRNAscan-SE [23], respectively. ...


Plasmid
Volume 74, July 2014, Pages 32–38 DOI: 10.1016/j.plasmid.2014.05.003

Construction of a Novel Inducible Expression Vector for Lactococcus lactis M4 and Lactobacillus plantarum Pa21.

Maidin M. S. T. et al.,
a Department of Cell and Molecular Biology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia b Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia

... The potential Pribnow box and -35 site of P hsp were predicted with BPROM (Softberry, USA), an online bacterial ? 70 promoter (major E. coli promoter class) recognition program with about 80% accuracy and specificity that can be accessed freely at (http://linux1.softberry.com ...


Journal of proteomics
2014, 108, 78-88. DOI: 10.1016/j.jprot.2014.05.005

Phosphate regulated proteins of Xanthomonas citri subsp. citri: A proteomic approach

Pegos, V. R., Nascimento, J. F., Sobreira, T. J. P., Pauletti, B. A., Paes-Leme, A., & Balan, A.
a Laboratorio Nacional de Biociencias — LNBio, Centro de Pesquisas em Energia e Materiais — CNPEM, Campinas, SP, Brazil b Universidade Estadual de Campinas — UNICAMP, Instituto de Biologia, Campinas, SP, Brazil

... the promoter regions of the X. citri Pho regulon genes, we submitted a sequence of 100 nucleotides upstream of the start codon of isolated genes or from the first gene belonging to an operon, to the bacterial promoter prediction programme BPROM from the SoftBerry server (http ...


PloS one
2014, 9(3), e90603. Volume DOI: 10.1371/journal.pone.0090603

Analysis of the Promoters Involved in Enterocin AS-48 Expression

Cebrian R et al.,
Departamento de Microbiologia, Facultad de Ciencias, Universidad de Granada, Granada, Spain

... as-48 or bac regions (GenBank KJ146793 and Y12234.1, and D85752.1, respectively [9], [6]) were analysed with the bioinformatic programs Promoter Prediction by Neural Network (NNPP) [31] (http://s.fruitfly.org/seq_tools/promoter?.html) and BPROM (Softberry Inc., Mount ...


Nature communications
2014 , 5. Article number: 4076 DOI: 10.1038/ncomms5076

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

Bailey, S. F., Hinz, A., Kassen, R.
Department of Biology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5

... Bent arrows indicate promoters predicted by the Softberry BPROM program ( http://linux1.softberry.com/berry.phtml). ...


Microbiology
February 2013 vol. 159 no. Pt 2 230-242 DOI:10.1099/mic.0.061614-0

A CsrA/RsmA translational regulator gene encoded in the replication region of a Sinorhizobium meliloti cryptic plasmid complements Pseudomonas fluorescens rsmA/E mutants

Betina Agaras †, Patricio Sobrero † and Claudio Valverde
Laboratorio de Bioquimica, Microbiologia e Interacciones Biologicas en el Suelo, Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, Roque Saenz Pena 352 – Bernal B1876BXD – Buenos Aires, Argentina

... The rsmA Sm coding sequence is shaded in dark grey. The sequence of the divergently encoded ORF II gene is shaded in light grey. Putative ? 70 -dependent promoters (boxed) were identified via the Softberry Bprom algorithm (http://linux1.softberry.com/berry.phtml). ...


PLOS ONE
February 08, 2013DOI: 10.1371/journal.pone.0056321

Generation of an Artificial Double Promoter for Protein Expression in Bacillus subtilis through a Promoter Trap System

Yang et al.,
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China Department of Animal Science, McGill University, Quebec, Canada

... The sequence analysis was performed online with NCBI blast 2.0 (www.ebi.ac.uk); promoter region was predicted by the BPROM program (Softberry Inc., Mount Kisco, NY, USA; http://linux1.softberry.com). Sub-cloning of promoter regions. ...


Microbiology
January 2013 vol. 159 no. Pt 1 96-106 DOI:10.1099/mic.0.062349-0

Transcriptional regulation of the Rhodobacter capsulatus response regulator CtrA

Molly M. Leung †, Cedric A. Brimacombe and J. Thomas Beatty
Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada

... Promoter sequence analysis, RNA 5?end-mapping and ?-galactosidase assays. Analysis of sequences for putative promoter –10 and –35 sites was done using the Softberry bacterial promoter prediction computer program BPROM (http://www.softberry.com/all.htm). ...


PloS one
February 13, 2013DOI: 10.1371/journal.pone.0056063

A Two-Component System (XydS/R) Controls the Expression of Genes Encoding CBM6-Containing Proteins in Response to Straw in Clostridium cellulolyticum

Celik et al.,
Aix-Marseille Universite, CNRS, UMR7283, Marseille, France Institut fur Mikrobiologie, Ernst-Moritz-Arndt Universitat, Greifswald, Germany

... D) Genetic organization of xydS/R and xyl-doc genes as in (A) with schematic localizations of promoters (thin arrow) and terminators (stem-loop) predicted by BPROM and FindTerm programs (http://linux1.softberry.com). doi:10.1371/journal.pone.0056063.g001. ...


F1000Research
2013, 2:99 (doi: 10.12688/f1000research.2-99.v1

Polycistronic transcription of fused cassettes and identification of translation initiation signals in an unusual gene cassette array from Pseudomonas aeruginosa [v1; ref status: approved with reservations 2, http://f1000r.es/p3]

Erica L Fonseca, Ana Carolina Paulo Vicente
Laboratorio de Genetica Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, 4365, Brazil - See more at: http://f1000research.com/articles/2-99#sthash.epID3u3g.dpuf

... The 5'UTR from gcu14 were submitted to the promoter predictor programs Neural Network for Promoter Prediction version 2.2 (Berkeley Drosophila Genome Project, http://www.fruitfly.org/ index.html) and BPROM (SoftBerry, http://linux1.softberry.com/berry.phtml). ...


PloS one
October 16, 2013 DOI: 10.1371/journal.pone.0076685

The Global Anaerobic Regulator Anr, Is Involved in Cell Attachment and Aggregation Influencing the First Stages of Biofilm Development in Pseudomonas extremaustralis

Paula M. Tribelli, Anthony G. Hay, Nancy I. Lopez
IQUIBICEN-CONICET and Dpto. de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina Department of Microbiology, Cornell University, Ithaca, New York, United States of America

... support [37], and in an intergenic genomic zone. Putative ? 70 dependent promoters were identified using the Softberry Bprom algorithm (http://linux1.softberry.com/berry. phtml). Sequence logos was performed using 5 Anr-boxes ...


Microbiology
September 2013 vol. 159 no. Pt 9 1911-1919 DOI: 10.1099/mic.0.064709-0

Identification and characterization of biofilm formation-defective mutants of Xanthomonas citri subsp. citri

Malamud et al.,
1Instituto de Ciencia y Tecnologia Dr Cesar Milstein, Fundacion Pablo Cassara, CONICET, Saladillo 2468, C1440FFX Ciudad de Buenos Aires, Argentina 2Embrapa Recursos Geneticos e Biotecnologia and Centro APTA Citros Sylvio Moreira, Instituto Agronomico de Campinas, Cordeiropolis, Sao Pablo, Brazil

... Tn5. An analysis was performed for each mutant, taking into account the relative position of the transposon and the presence of promoter regions predicted by BProm (Softberry, http://linux1.softberry.com/berry.phtml) (Fig. S2 ...


Microbiology
November 2013 mic.0.074773-0 DOI:10.1099/mic.0.074773-0

Exopolyphosphatase of Pseudomonas aeruginosa is essential for the production of virulence factors and its expression is controlled by NtrC and PhoB, acting at two interspaced promoters.

Gallarato et al.,
1 Dep Biologia Molecular, FCEFQyN, Universidad Nacional de Rio Cuarto; 2 Dep Ingenieria Celular y Biocatalisis, Inst Biotecnologia, UNAM, Cuernavaca

... PRODORIC was used to determine the Integration 182 Host Factor (IHF) consensus (Munch et al., 2003). The BPROM tool from the SoftBerry server 183 (http://linux1.softberry.com) was used to identify ?70-dependent promoters. NtrC and PhoB 184 ...


Antimicrob. Agents Chemother.
July 2013 vol. 57 no. 7 3430-3433 DOI:10.1128/AAC.00515-13

SatR Is a Repressor of Fluoroquinolone Efflux Pump SatAB

Escudero et al.,
Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spaina Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spainb

... Positive results were obtained for both strains, proving that satR is part of the satRAB operon (data not shown). Upstream from satRAB, we found two 9-bp pseudopalindromic regions overlapping the predicted ?10 box (BPROM software; Softberry) (Fig. ...


Archives of Virology
Volume 158, Issue 11 , pp 2409-2413 DOI:10.1007/s00705-013-1726-3

Genome sequence analysis of the Vibrio parahaemolyticus lytic bacteriophage VPMS1

Martin Ramirez-Orozco, Vania Serrano-Pinto, Norma Ochoa-Alvarez, Roman Makarov, Sergio F. Martinez-Diaz
1. Centro de Investigaciones Biologicas del Noroeste (CIBNOR), Instituto Politecnico Nacional, 195, Col. Playa Palo de Santa Rita Sur, 23096, La Paz, B.C.S, Mexico 2. Centro Interdisciplinario de Ciencias Marinas-IPN (CICIMAR), Av. Instituto Politecnico Nacional, s/n Col. Playa Palo de Santa Rita, 23096, La Paz, B.C.S, Mexico

... results were visually inspected. Results were taken as significant when e-values were under 0.01. Promoter candidates were determined using the BPROM 0.3.2 software (Softberry, Mount Kisco, NY). A CD search to identify ...


BMC Biotechnol.
2013; 13: 25. DOI: 10.1186/1472-6750-13-25

Development of a Fur-dependent and tightly regulated expression system in Escherichia coli for toxic protein synthesis

Lingyu Guan, 1 Qin Liu, 1 Chao Li,1 and Yuanxing Zhang 1
1State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P. R. China

... Its characteristic regions were demonstrated as the same result by three online promoter prediction tools-Softberry, BDGP and SCOPE. ... PfhuA characteristic regions were predicted by online tools: BPROM-bacterial promoter prediction program from Softberry ...


Tuberculosis
Volume 93, Issue 4, July 2013, Pages 389–397 DOI:10.1016/j.tube.2013.03.007

An insight into the regulation of mce4 operon of Mycobacterium tuberculosis

Rathor et al.,
a Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India b Medicinal Chemistry Division, Dr B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India

... (http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). To know fidelity of these softwares, known promoter sequences of purC (Rv0780), katG (Rv1908c), rpsl (Rv0682) and recA (Rv2737c) genes of M. tuberculosis were also analyzed. ...


Annals of Microbiology
August 2013 DOI:10.1007/s13213-013-0717-7

Characterization of the cryptic plasmid pWCZ from Lactobacillus paracasei WCZ isolated from silage

Yezhi Fu, Zhengyuan Zhai, Haoran An, Yanling Hao
1. Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China

... DNASTAR software package was employed to detect direct and inverted repeats. Putative promoter and terminator predictions were analyzed with BPROM and FindTerm, respectively (http://linux1.softberry.com/berry.phtml). ...


Biochemical and Biophysical Research Communications
Volume 435, Issue 1, 24 May 2013, Pages 28–33 DOI:10.1016/j.bbrc.2013.04.017

Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): Regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape

Hayashi et al.,
a Department of Food and Fermentation Science, Faculty of Food and Nutrition, Beppu University, Beppu 874-8501, Japan b Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan

... 4A. The translational start site, putative ribosomal binding site (RBS), putative –10, and –35 promoter elements of the sco5550 and sco5551 were found using the bacterial promoter predictor BPROM program (SoftBerry, Mt. ...


J. Bacteriol. December
2013 vol. 195 no. 23 5370-5380 DOI:10.1128/JB.00615-13

The sll1951 Gene Encodes the Surface Layer Protein of Synechocystis sp. Strain PCC 6803

Christoph Trautner and Wim F. J. Vermaas
School of Life Sciences, Arizona State University, Tempe, Arizona, USA

... A possible ribosome-binding site (AGGAG) is located at bp ?19 from the start codon, whereas the most probable ?10 and ?35 transcriptional signals, as predicted via BPROM (Softberry Inc., Mount Kisco, NY), appear to be distant at positions ?95 (TGCTATGAT) and ?114 ...


Appl. Environ. Microbiol.
February 2013 vol. 79 no. 4 1150-1159 DOI:10.1128/AEM.03556-12

Genomic Plasticity Enables a Secondary Electron Transport Pathway in Shewanella oneidensis

M. Schicklberger, G. Sturm and J. Gescher
Institute for Applied Biosciences (IAB), Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany

... (35). Promoter prediction.The BPROM bacterial promoter predictor was used to identify entire (?35/?10) putative promoter regions (SoftBerry, Mt. Kisco, NY). ... Analysis of the hybrid region by use of bioinformatic tools (BPROM; SoftBerry, Mt. ...


PloS one
October 07, 2013DOI: 10.1371/journal.pone.0076630

Evolutionary Insight into the Functional Amyloids of the Pseudomonads

Morten S. Dueholm, Daniel Otzen, Per Halkj?r Nielsen
Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aarhus, Denmark Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark

... to fapF. A promoter region containing -35 and -10 regions could be identified in front of the lone fapF in Chromobacterium using the prokaryotic promoter prediction tool Softberry-BPROM (http://linux1.softberry.com). No promoter ...


Biotechnology Letters
Volume 35, Issue 8 , pp 1331-1337 DOI:10.1007/s10529-013-1209-3

Expression of mosquito-larvicidal toxin genes under the control of a native promoter in Enterobacter amnigenus An11

Wachiraporn Toopaang, Boonsri Jongsareejit, Sumarin Soonsanga, Boonhiang Promdonkoy
1. Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand 2. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand

... Promoter sequence of the inserted fragment was analyzed using BPROM (http://linux1.softberry.com/berry.phtml) and BDGP (http://www.fruitfly.org/seq_tools/ promoter.html) programs. Measurement of GFP intensity. Enterobacter ...


PLoS Pathog
2013 June; 9(6): e1003428. DOI:10.1371/journal.ppat.1003428

A Novel Two-Component Signaling System Facilitates Uropathogenic Escherichia coli's Ability to Exploit Abundant Host Metabolites

Cai et al.,
1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America 2Laboratory Animal Resources, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America

... The promoter regions of c5032 and c5038 were predicted by BProm program (http://linux1.softberry.com) [45]. . ...


Extremophiles
Volume 17, Issue 5 , pp 809-819 DOI:10.1007/s00792-013-0562-4

Characterization of a cold-adapted and salt-tolerant esterase from a psychrotrophic bacterium Psychrobacter pacificensis

Guojie Wu, Gaobing Wu, Tao Zhan, Zongze Shao, Ziduo Liu
1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China 2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

... The open reading frame (ORF) and the promoter region in the obtained DNA fragments were analyzed by FGENSB and BPROM (http://linux1.softberry.com/berry.phtml), amino acid alignments by BLASTP (http://www.ncbi.nlm.nih.gov/), and Signal peptide by the SignaIP 4.0 ...


American Journal of Bioinformatics Research
2013; 3(2): 11-20 doi:10.5923/j.bioinformatics.20130302.01

nsilico Analysis of Novel hipAB, ccdBA, and yoeB-yefM Toxin-Antitoxin Homolog’s from the Genome of Xenorhabdus nematophila

Jitendra Singh Rathore, Mahendra Pal Singh, Pradeep Gautam
School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201308, India

... 2.5. Promoter Analysis. Identification of putative pro- moters associated with ORFs was determined by software BPROM (www.softberry.com). 2.6. Genomic DNA Isolation. X. nematophila culture was inoculated from glycerol stock in 50 ml and grown overnight at 28?, 200 rpm. ...


Microbiology
May 2013 mic.0.066332-0 DOI:10.1099/mic.0.066332-0

A modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius

Jeremy Bartosiak-Jentys, Ali H. Hussein, Claire J. Lewis and David J. Leak1
University of Bath

... 113 A 293nt DNA fragment containing the cellobiose specific phosphotransferase system operon's 114 promoter sequence (P?glu), predicted using BPROM software (SoftBerry), was amplified using primers 115 SalI_P?glu_F and XmaI_ClaI_P?glu_R. ...


Biochemical Genetics
Volume 51, Issue 9-10 , pp 766-779 DOI:10.1007/s10528-013-9605-x

Molecular Characterization of a Fungicidal Endoglucanase from the Cyanobacterium Calothrix elenkinii

Chitra Natarajan, Vishal Gupta, Kanika Kumar, Radha Prasanna
1. Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012, India 3. Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, 500007, Andhra Pradesh, India 2. National Research Centre for Plant Biotechnology, IARI, New Delhi, 110012, India

... For each sequence, SignalP-HMM reports the overall signal peptide probability, equal to the posterior probability of signal peptide (S) for position 1. The bacterial promoter prediction program BPROM (http://linux1.softberry.com/berry.html) was used to identify the position of the ...


Journal of Molecular Catalysis B: Enzymatic
Volume 98, 30 December 2013, Pages 119–126 DOI:10.1016/j.molcatb.2013.10.012

A novel esterase from a psychrotrophic bacterium Psychrobacter celer 3Pb1 showed cold-adaptation and salt-tolerance

Guojie Wu a, Shuo Zhang a, Houjin Zhang b, Shanshan Zhang a, Ziduo Liu a,
a State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China b School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430070, PR China

... of the esterase-encoding gene, est12, was carried out by Basic Local Alignment Search Tool (BLAST) program on the NCBI online database (http://www.ncbi.nlm.nih.gov), and the promoter region was analyzed by FGENSB and BPROM (http://linux1.softberry.com/berry.phtml ...


DNA Res
(2013) doi: 10.1093/dnares/dst050 First published online: November 25, 2013

Global Transcriptional Response to Heat Shock of the Legume Symbiont Mesorhizobium loti MAFF303099 Comprises Extensive Gene Downregulation

Ana Alexandre 1,2, Marta Laranjo 1,2 and Solange Oliveira 1
1ICAAM – Instituto de Ciencias Agrarias e Ambientais Mediterranicas (Laboratorio de Microbiologia do Solo), Universidade de Evora, Nucleo da Mitra, Ap. 94, 7002-554 Evora, Portugal 2IIFA – Instituto de Investigacao e Formacao Avancada, Universidade de Evora, Ap. 94, 7002-554 Evora, Portugal

... MicrobesOnline Operon Predictions (www.micro-besonline.org/operons/) was used for operon prediction. 36 The identification of putative promoter sequences was performed using BPROM-Prediction of bacterial promoters software (www.softberry.com). ...


J. Bacteriol.
September 2013 vol. 195 no. 18 4264-4273 DOI:10.1128/JB.00471-13

Gene Content and Diversity of the Loci Encoding Biosynthesis of Capsular Polysaccharides of the 15 Serovar Reference Strains of Haemophilus parasuis

Howell et al.,
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdoma The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdomb

... Each capsule locus was analyzed for the presence of promoters using BPROM (http://linux1. softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb), where the top scores were found and mapped to within 150 bp preceding the start codon of each CDS of ...


Russian Journal of Genetics
Volume 49, Issue 5 , pp 477-486 DOI:10.1134/S1022795413050116

Organization and maintenance features of IncP-7 naphthalene degradation plasmid pFME5 basic replicon

O. V. Volkova, I. A. Kosheleva, A. M. Boronin
19806. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia 29806. Pushchino State Educational Institute of Natural Sciences, Pushchino, 142290, Russia

... substituted nucleotides are underlined. Page 4. 480 RUSSIAN JOURNAL OF GENETICS Vol. 49 No. 5 2013 VOLKOVA et al. SOSUI, and BPROM (Softberry) software available online. RESULTS AND DISCUSSION pFME5 Basic ...


PloS one
January 28, 2013DOI: 10.1371/journal.pone.0054479

A Non-Classical LysR-Type Transcriptional Regulator PA2206 Is Required for an Effective Oxidative Stress Response in Pseudomonas aeruginosa

F. Jerry Reen, Jill M. Haynes, Marlies J. Mooij, Fergal O'Gara
BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland

... Genome sequences were obtained from the www.pseudomonas.com resource [24] and compared using the ARTEMIS Comparison Tool on the www.webact.org site [25]. Promoter predictions were performed using BProm software on the http://linux1.softberry.com site. ...


mBio
doi: 10.1128/mBio.00366-13 27 August 2013 vol. 4 no. 5 e00366-13

Vibrio cholerae ToxR Downregulates Virulence Factor Production in Response to Cyclo(Phe-Pro)

X. Renee Bina, Dawn L. Taylor, Amit Vikram, Vanessa M. Ante, James E. Bina
Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA

... encoding a hypothetical protein. Analysis of the leuO locus using BPROM promoter prediction software (http://www.softberry.com) indicated the presence of a single promoter upstream of VC2486. Consistent with this, VC2486 ...


Genome Biol Evol
(2013) 5 (2): 418-438. doi: 10.1093/gbe/evt008

Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

Gertraud Burger 1,*, Michael W. Gray 2, Lise Forget 1 and B. Franz Lang 1
1Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Universite de Montreal, Montreal, Quebec, Canada 2Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

... Potential bacteria-like promoters were predicted with BPROM (http://linux1.softberry.com), which was chosen among various public web-accessible predictors, because it yields for jakobid mtDNAs a reasonable number (in the order of 200) of potential sites per genome, instead ...


PloS one
October 21, 2013DOI: 10.1371/journal.pone.0076030

Divergent Control of Two Type VI Secretion Systems by RpoN in Pseudomonas aeruginosa

Thibault G. Sana, Chantal Soscia, Celine M. Tonglet, Steve Garvis, Sophie Bleves
Laboratoire d’Ingenierie des Systemes Macromoleculaires (UMR7255), CNRS & Aix-Marseille Univ, Marseille, France

... 2C). The BProm algorithm identified one ? 70 dependent promoter upstream of the lip3 gene and another, in the opposite direction, upstream of the hsiB3 gene (http://linux1.softberry.com/ berry.phtml??topic=bprom&group=programs&subgroup=gfin?db) (Fig. 2C). ...


BMC Genomics
2013, 14:73 doi:10.1186/1471-2164-14-73

Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera

Lilia Brinza 123, Federica Calevro 1 and Hubert Charles 12
1 UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INSA-Lyon, INRA, Universite de Lyon, Villeurbanne, France 2 BAMBOO, INRIA Rhone-Alpes, Montbonnot Saint-Martin, France 3 Present address: Universite de Lyon, Universite Lyon1, CNRS, UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, Lyon, France

... Promoters and transcription starts were predicted, in the four Buchnera strains, using the software BPROM © (http://linux1.softberry.com/berry.phtml webcite) and MacVector (MacVector, Cary, NC, USA) for ? 70 and ? 32 promoters, respectively. ...


Microbiology
June 2013 vol. 159 no. Pt 6 1097-1108 DOI:10.1099/mic.0.065763-0

Identification of multiple putative S-layer genes partly expressed by Lysinibacillus sphaericus JG-B53

Lederer et al.,
1Helmholtz-Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany 2Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany

... Miller, 1991). The analyses of the promoter regions were performed with the program BPROM (http://linux1.softberry.com/berry.phtml?topic=bprom&group= programs&subgroup=gfindb; Solovyev & Shahmuradov, 2003). The ...


Microbiology
April 2013 vol. 159 no. Pt 4 737-747 DOI:10.1099/mic.0.064782-0

Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilms

Simmons et al.,
1Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA 2Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA

... Artemis (version 14.0.0; Wellcome Trust Sanger Institute). Promoter sequences were analysed using bprom (Prediction of Bacterial Promoters; http://linux1.softberry.com). The genome reference sequences for M. pneumoniae ...


Appl. Environ. Microbiol.
June 2013 vol. 79 no. 11 3494-3502 DOI:10.1128/AEM.03693-12

Identification and Expression of Genes Involved in the Conversion of Daidzein and Genistein by the Equol-Forming Bacterium Slackia isoflavoniconvertens

Christine Schroder a, Anastasia Matthies a, Wolfram Engst b, Michael Blaut a and Annett Braune a
Department of Gastrointestinal Microbiologya Analytics Group,b German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany

... blast). Searching for putative transcription promoter and terminator sequences was done using the Web-based programs BPROM (Softberry, Mount Kisco, NY) and ARNold (http://rna.igmors.u-psud.fr/toolbox/arnold), respectively. ...


J. Bacteriol.
April 2013 vol. 195 no. 7 1504-1514 DOI:10.1128/JB.01999-12

Identification of the Mutation Responsible for the Temperature-Sensitive Lipopolysaccharide O-Antigen Defect in the Pseudomonas aeruginosa Cystic Fibrosis Isolate 2192

Michael R. Davis Jr et al.,
aDepartment of Microbiology, Immunology, and Cancer Biology, University of Virginia Health Sciences Center, Charlottesville, Virginia, USA bComplex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA

... The deletion in this strain was verified by PCR and sequencing. Promoter identification.An approximately 1 kb sequence located directly 5? of the wbpM start codon was scanned for promoters by using the neural network promoter prediction program BPROM (Softberry). ...


PloS one
October 02, 2013DOI: 10.1371/journal.pone.0076198

Pseudomonas putida AlkA and AlkB Proteins Comprise Different Defense Systems for the Repair of Alkylation Damage to DNA – In Vivo, In Vitro, and In Silico Studies

Mielecki et al.,
Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia

... Also, the putative -35 and -10 boxes responsible for RNA polymerase interaction are marked in pink (retrieved from RegulonDB, http://regulondb.ccg.unam.mx) or grey (SoftBerry BPROM prediction tool, http://linux1.softberry.com). ...


Appl. Environ. Microbiol.
July 2013 vol. 79 no. 13 3967-3973 DOI:10.1128/AEM.00867-13

Biofilm Formation by Psychrobacter arcticus and the Role of a Large Adhesin in Attachment to Surfaces

Shannon M. Hinsa-Leasur a, Cassandra Koid a, James M. Tiedj b and Janna N. Schultzhaus a
Biology Department, Grinnell College, Grinnell, Iowa, USAa Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USAb

... with 64 bp separating the two genes. Based on results of the sequence analysis programs FGENESB and BPROM (SoftBerry), the Psyc_1602-encoding gene and cat1 reside in an operon. Located 379 bp downstream of cat1 ...


AEM
01197-13 DOI:10.1128/AEM.01197-13

Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 trigger alternative transcriptional host responses

Stuart Ainsworth 1, Aldert Zomer 2, Jennifer Mahony 1 and Douwe van Sinderen 1, 3
1Department of Microbiology, University College Cork, Western Road, Cork, Ireland 2Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 3Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Western Road, Cork, Ireland

... orf10. Analysis using BPROM 208 (http://www.softberry.com/berry.html) suggests a previously undetected promoter upstream of 209 orf10 (with proposed -35 and (extended) -10 sequences that correspond to ATGTAT and 210 ...


Plant Cell, Tissue and Organ Culture (PCTOC)
Volume 113, Issue 3 , pp 387-396 DOI:10.1007/s11240-012-0278-7

Plant tissue-specific promoters can drive gene expression in Escherichia coli

Jopcik et al.,
1. Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, P.O. Box 39A, 950 07, Nitra, Slovak Republic 2. Animal Production Research Centre, 951 41, Nitra, Slovak Republic 3. Constantine the Philosopher University, 949 74, Nitra, Slovak Republic

... elements and are capable to trigger gene expression in E. coli, we analyzed the sequences of DNA fragments carrying the plant embryo- and/or pollen-specific promoters using the bacterial sigma70 promoter recognition program BPROM (http://linux1.softberry.com/berry.phtml ...


J. Basic Microbiol.
doi: 10.1002/jobm.201300037

Multiple pqqA genes respond differently to environment and one contributes dominantly to pyrroloquinoline quinone synthesis.

Ge et al.,
1Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China 2School of Life Science and Biochemical Pharmaceutical, Shenyang Pharmaceutical University, Shenyang, China

... S2c), indicating that the transcriptional regulation events of these five genes were likely to be different. A high-score of putative prokaryotic promoter and regulation elements were predicted upstream of the coding sequence of ppqA2 by BProm software (www.softberry.com). ...


World Journal of Microbiology and Biotechnology
Volume 29, Issue 11 , pp 2067-2076 DOI:10.1007/s11274-013-1370-9

Characterization of a serine hydroxymethyltransferase for l-serine enzymatic production from Pseudomonas plecoglossicida

Wei Jiang, Bingzhao Xia, Junjie Huang, Ziduo Liu
1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

... 1 Phylogenetic tree of PplglyA. The immediate upstream sequence from the ORF was analyzed; the promoter of the glyA gene was predicated by the tool of the Prediction of bacterial promoters (BPROM, http://linux1.softberry.com); and the putative ?10 box (GGTTAGAAT, from ...


Plasmid
Volume 70, Issue 1, July 2013, Pages 52–60 DOI:10.1016/j.plasmid.2013.01.006

Role of plasmid- and chromosomally encoded Hha proteins in modulation of gene expression in E. coli O157:H7

Sonia Paytubi a, Manuela Dietric b, Mario H. Queiroz b, Antonio Juarez a, b
a Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain b Institut de Bioenginyeria de Catalunya (IBEC), Baldiri i Reixac 10-12, 08028 Barcelona, Spain

... Promoter region was analysed via the BPROM program developed by Softberry, which predicted two promoters for the hha pO157 gene (TTTTCA-15bp-TCGTAT and TGGAGA-17bp-TGGCAA) with the respective Pribnow boxes located at positions -243 and -36 relative to the ...


Molecular Plant Pathology
14: 119–130. February 2013 doi: 10.1111/j.1364-3703.2012.00835.x

The ESX/type VII secretion system modulates development, but not virulence, of the plant pathogen Streptomyces scabies

Fyans, J. K., Bignell, D., Loria, R., Toth, I. and Palmer, T.
1Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK 2James Hutton Institute, Invergowrie, Dundee, UK

... carrying esxA and esxB, together with 225 base pairs upstream of esxA, which should cover the natural promoter region (predicted to lie approximately 100 base pairs upstream of the esxA start codon according to the bprom prediction program; http://linux1.softberry.com/berry ...


PloS one
October 25, 2013DOI: 10.1371/journal.pone.0076341

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

Crost et al.,
The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom Laboratoire de Chimie Bacterienne, Institut de Microbiologie de la Mediterranee, CNRS and Aix-Marseille University, Marseille, France

... Prediction of the promoters was performed using the BPROM program (http://linux1.softberry. com/berry.phtml??topic=bprom&group=programs&subgroup=gfin?db). Results. Comparative analysis of R. gnavus E1 and R. gnavus ATCC 29149 glycobiome. ...


RNA
2013. 19: 1341-1348 DOI:10.1261/rna.038794.113

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Matelska et al.,
1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland 2Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland

... was analyzed. Full sequence alignment is available as Supplemental File 1. ? 70 promoters associated with the representative motifs (Fig. 2) were predicted with BPROM (http://linux1.softberry.com/berry.phtml). To estimate ...


ACS Synth. Biol.
2013, 2 (2), pp 111–120 DOI: 10.1021/sb300114d

Promoter Element Arising from the Fusion of Standard BioBrick Parts

Yao et al.,
†Department of Biomedical Engineering, ‡UC Davis Genome Center, and §Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, United States Cellular and Molecular Biology Program, University of Michigan, 1011 North University Avenue, Ann Arbor, Michigan 48109, United States

... in silico methods for detecting pKAT or pKAT-like promoters, we examined the DNA sequence composed of 200 base pairs flanking either side of the barcode (for a 425 bp total sequence) in BBa_K327001 with the following algorithms: BPROM (http://www.softberry.com/berry ...


J. Bacteriol.
November 2013 vol. 195 no. 22 5025-5040 DOI:10.1128/JB.00669-13

Phosphate Concentration and the Putative Sensor Kinase Protein CckA Modulate Cell Lysis and Release of the Rhodobacter capsulatus Gene Transfer Agent

Westbye et al.,
Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

... 2A). Analysis of the region upstream of ORF g1 using the bioinformatic tool BPROM (Softberry) indicated putative ?10 and ?35 sequences (light green in Fig. 2A). However, the location of these sequences did not correspond to either of the two RNA 5? ends mapped. ...


Molecular Microbiology
(2013), 88: 936–950. doi: 10.1111/mmi.12234

Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I

Ozyamak, E., de Almeida, C., de Moura, A. P. S., Miller, S. and Booth, I. R.
1School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK 2Institute of Complex Systems & Mathematical Biology, School of Natural & Computer Sciences, University of Aberdeen, Aberdeen, UK

... Averages from two independent experiments are shown. Black arrows indicate locations of known promoters. Gray arrows indicate promoters predicted by BPROM (http://linux1.softberry.com). Data smoothing and labels are as described in Fig. 3. Download figure to PowerPoint. ...


The Journal of Pathology
DOI:10.1002/path.4313

Versatile and enhanced tumour modeling in mice via somatic cell transduction

Rodriguez et al.,
1CRUK Cambridge Institute, Department of Molecular Imaging, University of Cambridge, Li Ka Shing Centre, Cambridge, UK 2Histopathology Department, Addenbrookes Hospital, Cambridge, UK

... Nat Protoc 2009; 4: 495-505. 14. BPROM: Available from: http://linux1.softberry.com/berry.phtml? topic=bprom&group=programs&subgroup=gfind b 15. BDGP Neural Network Promoter Prediction: Available from: http://www.fruitfly.org/seq_tools/promoter.html 16. ...


PLoS One.
2013; 8(9): e74495. doi: 10.1371/journal.pone.0074495

Determination of sRNA Expressions by RNA-seq in Yersinia pestis Grown In Vitro and during Infection

Yan et al.,
1State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China 2Microbiology Laboratory, Sichuan Agricultural University, Yaan, Sichuan province, China

... were further removed. Bacterial promoter regions were predicted by BPROM (http://linux1.softberry.com/) and Neural Network Promoter Prediction program (http://www.fruitfly.org/seq_tools/promoter.html). Rho-independent transcription ...


J. Bacteriol.
April 2013 vol. 195 no. 8 1834-1844 DOI:10.1128/JB.01946-12

Sigma Factor RpoS Controls Alkylresorcinol Synthesis through ArpR, a LysR-Type Regulatory Protein, during Encystment of Azotobacter vinelandii

Yanet Romero, Soledad Moreno, Josefina Guzman, Guadalupe Espin and Daniel Segura
Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico

... By using the bacterial promoter recognition program BPROM (http://www.softberry.com/berry. phtml?topic=bprom&group=programs&subgroup=gfindb), ?35 and ?10 promoter elements showing similarity to RpoD-dependent promoters were identified in the arsA upstream region ...


Biotechnol. Bioeng.
(2013), 110: 2959–2969. doi: 10.1002/bit.24954

Isolation of fully synthetic promoters for high-level gene expression in Corynebacterium glutamicum.

Yim, S. S., An, S. J., Kang, M., Lee, J. and Jeong, K. J.
1Department of Chemical and Biomolecular Engineering, KAIST, Daejeon, Republic of Korea 2Department of Food Science & Biotechnology, Kyungsung University, Busan, Korea 3Institute for the BioCentury, KAIST, Daejeon, Republic of Korea

... All clones were 74 bp long, except for clone I29 that contained one more base in the promoter region, which might have been inserted during synthesis with the random primer (Synpro-F). BPROM software (http://www.softberry.com/berry.phtml) successfully predicted the ...


BMC Biotechnology
2013, 13:22 http://www.biomedcentral.com/1472-6750/13/22

Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with b-glucosidase, b-fucosidase and b-galactosidase activities

Anna Wierzbicka-Wos 1†, Paulina Bartasun2†, Hubert Cieslinski2* and Jozef Kur2
1 Department of Microbiology, Faculty of Biology, University of Szczecin, Felczaka 3c, Szczecin 71-412, Poland. 2 Department of Microbiology, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-233, Poland.

... As described on the BProm website, the program has an E. coli promoter recognition accuracy of approximately 80%, and the most recent version is accessible at http://linux1.softberry.com/ berry.phtml?topic=bprom&group=programs &subgroup=gfindb. ...


Phil. Trans. R. Soc. B
19 April 2013 vol. 368 no. 1616 20120317 DOI:10.1098/rstb.2012.0317

Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi

Wagner et al.,
1Institute of Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle 06099, Germany 2Helmholtz Centre for Environmental Research, UfZ Leipzig, Leipzig 04318, Germany 3Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, The Netherlands

... start sites; the short arrows above the inverted repeat sequences represent the putative recognition sequences of the regulator; bold and italic letters depict the consensus sequences of the ?10 and ?35 region predicted by the BPROM software (http://linux1.softberry.com/berry ...


International journal of molecular sciences
2013, 14(8), 16901-16916. DOI:

Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

Banderas A., Guiliani N.
Laboratory of Bacterial Communication, Department of Biology, Faculty of Sciences, University of Chile, Santiago 780-0024, Chile

... Manipulation Suite [50] and FaBox [51]. Consensus sigma 70 bacterial promoter -10 and -35 elements were inferred using the Bprom predictor (www.softberry.com) Type I and Type II PBS sequences with additional 100 bp flanking each side ware used as input for Bprom. ...


Genetics and Molecular Biology
(2013). 36(2), 243-251. DOI:

Characterization of the omlA gene from different serotypes of Actinobacillus pleuropneumoniae: a new insight into an old approach

Rossi, C. C., Araujo, E. F. D., Queiroz, M. V. D., & Bazzolli, D. M. S.
Laboratorio de Genetica Molecular de Micro-organismos, Departamento de Microbiologia, Universidade Federal de Vicosa, Vicosa, MG, Brazil

... pseudogenes. Nucleic Acids Res 31:5338-5348. Internet Resources Bacterial Promoter Prediction Program BPROM, http://www.softberry.com (March 16, 2013). Associate Editor: Celia Maria de Almeida Soares License information ...


PloS one
(2013). 8(4), e61808. DOI:

Characterization of the Biocontrol Activity of Pseudomonas fluorescens Strain X Reveals Novel Genes Regulated by Glucose

Kremmydas, G. F., Tampakaki, A. P., & Georgakopoulos, D. G.
Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece

... The putative promoter site prediction was performed with two bioinformatic applications, BPROM software (Softberry Inc., Mount Kisco, NY, USA) and NNPP 2.2 software (Berkeley Drosophila Genome Project-BDGP, Berkeley, CA, USA). ...


Scientific reports
(2013). 3.e DOI:10.1038/srep02240

Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles

ThLongkumer et al.,
Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India Dept. of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad – 500 046, India Bioinformatics Centre, Pondicherry University, Puducherry - 605 014, India

...and for promoter prediction, BPROM software (www.softberry.com/berry.phtml?topic=bprom) was used. ...


World Journal of Microbiology and Biotechnology
Volume 28, Issue 5 , pp 2221-2228, DOI: 10.1007/s11274-012-1029-y

Identification of a copper-responsive promoter and development of a copper biosensor in the soil bacterium Achromobacter sp. AO22

Shee Ping Ng (1) (2), Enzo A. Palombo (1), Mrinal Bhave (1)
1. Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Melbourne, VIC, 3122, Australia 2. School of Science and Technology, Nilai University College, Persiaran Kolej Bbn, 71800, Putra Nilai, Negeri Sembilan, Malaysia

... AO22 (Ng et al. 2012; Genbank num- ber GU929214) contains a 255 bp region between the proposed start codons of copR and copA (Fig. 1). Analysis by BPROM (http://linux1.softberry.com/ berry.phtml?topic= bprom&group=programs&subgroup=gfindb) (Ng et al. ...


Antonie van Leeuwenhoek
March 2012, Volume 101, Issue 3, pp 583-593 DOI 10.1007/s10482-011-9673-z

Gene expression modulation by heat stress in Acidithiobacillus ferrooxidans LR

Daniela A. Ribeiro, Lucio F. C. Ferraz, Renato Vicentini, Laura M. M. Ottoboni
1. Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas—UNICAMP, C.P. 6010, Campinas, SP, 13083-875, Brazil

... 0.05). Bioinformatic analysis BPROM (Softberry, Inc.) was used to predict the transcription start site of the genes. BPROM is a bacterial r70 promoter recognition software program, which has about 80% accuracy and specificity. ...


Molecular Biology
July 2012, Volume 46, Issue 4, pp 542-547 DOI 10.1134/S0026893312030120

Structure of replication initiation region in Pseudomonas IncP-7 streptomycin resistance plasmid Rms148

O. V. Volkova, I. A. Kosheleva, A. M. Boronin
1. Pushchino State University, Pushchino, 142290, Russia 2. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia

... Russia). Nucleotide and amino acid sequences were analyzed using DnaStar, BLAST, Jred3, PredictProtein, and BPROM software (Softberry). CLUSTAL and TREECON programs were used to determine the phylogenetic tree [10]. ...


J Microbiol Biotechnol.
2012 Jun;22(6):742-53.

The heavy metal tolerant soil bacterium Achromobacter sp. AO22 contains a unique copper homeostasis locus and two mer operons

NS Ping, Palombo EA, Bhave M
Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Melbourne, Victoria 3122, Australia.

... DNA regions of interest were submitted in both directions to the BPROM server (http://linux1. softberry.com/ berry.phtml?topic=bprom&group=programs&subgroup=gfindb) for predicting potential promoter regions including the -10 and -35 hexamers and likely transcription ...


The Journal of General and Applied Microbiology
Vol. 58 (2012) No. 5 p. 387-395 DOI: 10.2323/jgam.58.387

An examination of an Antarctic soil metagenomic-derivate putative methylthioadenosine phosphorylase gene as a novel reporter gene for promoter trapping

Paulina Bartasun 1), Hubert Cieslinski 1), Jozef Kur 1)
1) Department of Microbiology, Chemical Faculty, Gdansk University of Technology

... BProm has about 80% accuracy in E. coli pro- moter recognition as was described at its website. The recent version of BProm is accessible from the website (http://linux1.softberry. com/berry.phtml?topic=bprom& group=programs&subgroup=gfindb). ...


Journal of Industrial Microbiology & Biotechnology
May 2012, Volume 39, Issue 5, pp 731-741 DOI: 10.1007/s10295-011-1074-9

Cloning and characterization of two new thermostable and alkalitolerant a-amylases from the Anoxybacillus species that produce high levels of maltose

Yen Yen Chai et al.,
1. Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia 2. Enzyme and Microbial Technology Research, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

... html). The putative ribosome binding site was identified by a sequence comparison with the corresponding regions of other a-amylase genes. The promoter regions were pre- dicted using the BPROM program (http://linux1.softberry. ...


Antimicrob. Agents Chemother.
January 2012 vol. 56 no. 1 464-471 DOI: 10.1128/AAC.00602-11

Identification of Hopanoid Biosynthesis Genes Involved in Polymyxin Resistance in Burkholderia multivorans

Rebecca J. Malott, Barbara R. Steen-Kinnaird, Tracy D. Lee and David P. Speert
Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada

.. Lynnon Biosoft, Vaudreuil, Quebec, Canada). Additional in silico promoter and terminator predictions were performed with BPROM and FindTerm (Softberry, Inc., Mount Kisco, NY). Sequence similarity searches were performed ...


Current Microbiology
December 2012, Volume 65, Issue 6, pp 770-775 DOI: 10.1007/s00284-012-0228-y

Evidence for Two Promoters Internal to the Alginate Biosynthesis Operon in Pseudomonas aeruginosa

Janice L. Paletta, Dennis E. Ohman
1. Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, P.O. Box 980678, Richmond, VA, 23298-0678, USA 2. McGuire Veterans Affairs Medical Center, Richmond, VA, 23249, USA

... The intergenic spaces upstream of algG, algX, algL, algI, algJ, algF, and algA were analyzed using BPROM software (Softberry, Inc., Mount Kisco, NY) to identify a sigma-70 bacterial promoter consensus sequence, but none was found. ...


Appl. Environ. Microbiol.
February 2012 vol. 78 no. 3 828-838 DOI: doi: 10.1128/AEM.07480-11

Role of IncP-1b Plasmids pWDL7::rfp and pNB8c in Chloroaniline Catabolism as Determined by Genomic and Functional Analyses

Krol et al.,
aDepartment of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA bDepartment of Microbiology, University of California, Davis, Davis, California, USA

... Van der Auwera, unpublished data), with identity scoring by ClustalW. The pdca promoter region was analyzed using BPROM (Softberry Inc., Mount Kisco, NY). To infer the phylogenetic relationships of various IncP-1 plasmids ...


Microbiology
November 2012 mic.0.061614-0 DOI: 10.1099/mic.0.061614-0

A CsrA/RsmA translational regulator gene encoded in the replication region of a Sinorhizobium meliloti cryptic plasmid complements Pseudomonas fluorescens rsmA/E mutants

Betina Agaras, Patricio Sobrero and Claudio Valverde 1
Universidad Nacional de Quilmes

... by a typical AG-rich Shine-Dalgarno motif and by a putative ?70-dependent promoter 207 identified by the Bprom algorithm (http://linux1.softberry.com/berry.phtml), which may 208 drive rsmASm expression (Fig. 1). A second divergent ?70-dependent promoter was 209 ...


Research in Microbiology
Volume 163, Issues 6–7, July–August 2012, Pages 413–418 DOI: 10.1016/j.resmic.2012.05.006

Two sRNA RyhB homologs from Yersinia pestis biovar microtus expressed in vivo have differential Hfq-dependent stability

Zhongliang Deng et al.,
a Southern Medical University, Guangdong 510450, China b State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

... than E. coli ryhB RNA (Masse and Gottesman, 2002). The corresponding promoter regions including the -10 and -35 boxes were predicted using BPROM (http://linux1.softberry.com). RyhB1 and RyhB2 in Y. pestis contain the ...


Microbiological Research
Volume 168, Issue 2, 22 February 2013, Pages 113–118 DOI: 10.1016/j.micres.2012.07.003

Regulation of Staphylococcus aureus immunodominant antigen B (IsaB)

Nicole M. Mackey-Lawrence , Kimberly K. Jefferson
Department of Microbiology and Immunology, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA 23928, USA

... analysis. As Fig. 2 indicates, the TSS matched the TSS predicted by BPROM (Softberry software). The TSS was 39 bp upstream from the start codon, indicating that the isaB transcript contains a 39 nt 5?-untranslated region. ...


RNA
2012. 18: 795-806 DOI: 10.1261/rna.029868.111

Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase

Alfonso Benitez-Paez 1,2, Magda Villarroya 1 and M.-Eugenia Armengod 1,3
1Laboratorio de Genetica Molecular, Centro de Investigacion Principe Felipe, 46012 Valencia, Spain 2Bioinformatic Analysis Group–GABi, Centro de Investigacion y Desarrollo en Biotecnologia, Bogota D.C. 111221, Colombia

... The top of the figure shows a schematic of the chromosomal region including the mnmG-rsmG operon and the predictions of the promoter regions by the Neural Network Promoter Prediction (black) (Reese 2001) and BPROM (gray) (http://www.softberry.com/berry.phtml) servers. ...


Clinical Microbiology and Infection
Volume 18, Issue 11, pages E446–E451, November 2012 DOI: 10.1111/j.1469-0691.2012.03979.x

ISAba825 controls the expression of the chromosomal blaOXA-51-like and the plasmid borne blaOXA-58 gene in clinical isolates of Acinetobacter baumannii isolated from the USA

B. S. Lopes, L. Al-Hassan, S. G. B. Amyes
Medical Microbiology, The University of Edinburgh, Edinburgh, UK.

... four isolates. A putative promoter was found with ?35 (TTGTCA) and ?10 (TATGAA) located 17 bp apart from each other (BPROM, Softberry, Inc., Mount Kisco, NY) located 97 and 74 bp upstream of the bla OXA-65 gene. A target ...


J. Bacteriol.
July 2012 vol. 194 no. 13 3486-3494 DOI: 10.1128/?JB.00194-12

SMU.152 Acts as an Immunity Protein for Mutacin IV

Mohammad Shahnoor Hossain and Indranil Biswas
Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA

... Sequence analysis, confirmed using BPROM online software (prediction of bacterial promoters [Softberry]), indicates the presence of putative ?35 (TTAGAA) and ?10 (TATACT) box motifs 78 and 55 bp, respectively, upstream of the putative start codon with a putative ribosomal ...


J. Virol
2012, 86(23):12625. DOI: 10.1128/JVI.01783-12

Characterization of the genome, proteome and structure of yersiniophage ?R1-37

Skurnik et al.,
1Department of Bacteriology and Immunology, Infection Biology Research Programme, Haartman Institute, University of Helsinki, Helsinki, Finland 2Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland

... The PHIRE program was used to identify 159 repeat sequences in the phage genome (27). Bacterial promoter sequence identification was 160 carried out online at (http://linux1.softberry.com/berry.phtml) using the BPROM program. ...


MicrobiologyOpen
DOI: 10.1002/mbo3.53 Early View (Online Version of Record published before inclusion in an issue)

Unique secreted–surface protein complex of Lactobacillus rhamnosus, identified by phage display

Gagic, D., Wen, W., Collett, M. A. and Rakonjac, J.
1 Institute of Molecular BioSciences, Massey University, Palmerston North 4442, New Zealand 2 Fonterra Research and Development Centre, Palmerston North 4442, New Zealand

... Upstream of the transcriptional site a - 10 box (ACATAAAAT) and -35 box (TTGATT) was iden- tified in the putative promoter region using BPROM pro- moter prediction program from the Softberry server (http://www.softberry.com/berry.phtml). ...


Antimicrob Agents Chemother.
2012 Nov;56(11):5520-7. doi: 10.1128/AAC.01206-12. Epub 2012 Aug 13.

The putative lactococcal extracytoplasmic function anti-sigma factor llmg2447 determines resistance to the cell wall-active bacteriocin lcn972.

Roces et al.,
1 DairySafe Group, Department of Technology and Biotechnology of Dairy Products, IPLA-CSIC, Villaviciosa, Asturias, Spain. 2 Department of Molecular Genetics. Groningen Biomolecular Sciences and Biotechnology Institute. University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands

... 8 and Pfam (http://pfam.sanger.ac.uk/). ?70 promoter sequences were identified using Bprom 163 (http://www.softberry.com). Protein topology was predicted with TMHMM Server v2.0 164 (http://www.cbs.dtu.dk/services/TMHMM-2.0/) and SOSUI (http://bp.nuap.nagoya- 165 ...


PLoS ONE
7(10): e46587. doi:10.1371/journal.pone.0046587

QsdH, a Novel AHL Lactonase in the RND-Type Inner Membrane of Marine Pseudoalteromonas byunsanensis Strain 1A01261.

Wei Huang et al.,
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China

...The positive DNA fragment was analyzed with DNASTAR software (DNASTAR, Inc.) and by BLAST (http://www.ncbi.nlm.nih.gov/), BPROM (http://linux1.softberry.com/berry.phtml)...


Journal of Industrial Microbiology & Biotechnology
Volume 39, Issue 8 , pp 1245-1251 DOI: 10.1007/s10295-012-1128-7

Isolation and characterization of a novel GH67 a-glucuronidase from a mixed culture

Lee et al.,
1. USDA-ARS-WRRC, 800 Buchanan Street, Albany, CA, 94710, USA 2. Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Ministry of Education, China Three Gorges University, Yichang, 443002, China

... Page 4. J Ind Microbiol Biotechnol 123 When the upstream 5! region of the gene was analyzed by a bacterial promoter search program (BPROM, Softberry, Inc., Mount Kisco, NY, USA), ?35 and ?10 promoter ele- ments were identified (Fig. ...


Applied Microbiology and Biotechnology
Volume 94, Issue 1 , pp 261-272 DOI:10.1007/s00253-011-3621-8

Identification of the flavin monooxygenase responsible for ipso substitution of alkyl and alkoxyphenols in Sphingomonas sp. TTNP3 and Sphingobium xenophagum Bayram

Porter et al.,
1. Department of Microbiology, Cornell University, Ithaca, New York, NY, USA 2. Department of Environmental Science, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA

... 1997), was used as a template for the model. Sequences outside the opdA coding sequence were compiled as described above. Putative promoter regions were identified with the BPROM program (Softberry, Inc., Mount Kisco, NY). Nucleotide sequence ...


Infect. Immun.
September 2012 vol. 80 no. 9 3247-3255 DOI: 10.1128/IAI.00178-12

Role of RelA and SpoT in Burkholderia pseudomallei Virulence and Immunity

Muller et al.,
a College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, Devon, United Kingdom b London School of Hygiene and Tropical Medicine, London, United Kingdom

... In silico analyses.Homologies between amino acid sequences were determined using NCBI's BLASTP algorithm. Conserved domains were analyzed using NCBI's conserved domain database (CDD). Promoter predictions were performed using the Bprom software (Softberry). ...


AEM
Published ahead of print 7 September 2012, doi: 10.1128/AEM.01693-12

Whole genome microarray and gene deletion studies reveal regulation of the polyhydroxyalkanoate production cycle by the stringent response in Ralstonia eutropha H16

Christopher J. Brigham 1, Daan R. Speth 1,2, ChoKyun Rha 3 and Anthony J. Sinskey 1,4,5
1Department of Biology 2Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands

... and further analyzed using MEGA 5 (61). Potential ?54 promoters were manually identified 211 based on the consensus sequence published previously (3). Potential ?70 promoters were 212 identified using BPROM (Softberry). 213 Microarray data accession number. ...


J. Bacteriol.
April 2012 vol. 194 no. 8 1968-1978 DOI: 10.1128/?JB.00037-12

Transcriptional Organization and Physiological Contributions of the relQ Operon of Streptococcus mutans

Jeong Nam Kim, Sang-Joon Ahn, Kinda Seaton, Steven Garrett and Robert A. Burne
Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA

... Transcriptional organization of the relQ operon.Two potential promoters were identified 56 bp and 35 bp upstream of the relQ and pta start sites, respectively, using BPROM bacterial promoter identification software (Softberry, Inc., NY) (Fig. ...


Biological and Pharmaceutical Bulletin
Vol. 35 (2012) No. 4 P 573-581 DOI: 10.1248/bpb.35.573

Metabolism of Ginsenoside Rb1 by Human Intestinal Microflora and Cloning of Its Metabolizing b-D-Glucosidase from Bifidobacterium longum H-1

Il-Hoon Jung 1), Jeong Hoon Lee 1), Yang-Jin Hyun 1), Dong-Hyun Kim 1
1) Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University

... The putative sigma 70 type promoter sequences of both TTTACA (resembling ?35 se- quence) and GGTTATTAT (resembling ?10 sequence) were identified to be located at positions ?75 and ?55, respectively by using BPROM (http://linux1.softberry.com/berry.phtml?to pic ...


Infect. Immun.
2012, 80(9):3247. DOI: 10.1128/IAI.00178-12

Role of RelA and SpoT in Burkholderia pseudomallei Virulence and Immunity

Muller et al.,
College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, Devon, United Kingdom, a and London School of Hygiene and Tropical Medicine, London, United Kingdomb

... BLASTP algorithm. Conserved domains were analyzed using NCBI's conserved domain database (CDD). Promoter predictions were performed using the Bprom software (Softberry). Statistical analyses. Differences between ...


Molecular Plant Pathology
Volume 14, Issue 2, pages 119–130, February 2013 DOI: 10.1111/j.1364-3703.2012.00835.x

The ESX/type VII secretion system modulates development, but not virulence, of the plant pathogen Streptomyces scabies

Joanna K. Fyans 1,2, Dawn Bignell 3, Rosemary Loria 4, Ian Toth 2, Tracy Palmer 1
1Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK 2James Hutton Institute, Invergowrie, Dundee, UK

... carrying esxA and esxB, together with 225 base pairs upstream of esxA, which should cover the natural promoter region (predicted to lie approximately 100 base pairs upstream of the esxA start codon according to the bprom prediction program; http://linux1.softberry.com/berry ...


J. Bacteriol.
April 2012 vol. 194 no. 7 1789-1799 doi: 10.1128/JB.06827-11

Autoregulation of the Synthesis of the MobM Relaxase Encoded by the Promiscuous Plasmid pMV158

Fabian Lorenzo-Diaz a,*, Virtu Solano-Collado a, Rudi Lurz b, Alicia Bravo a and Manuel Espinosa a
aCentro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Madrid, Spain bMax Planck Institut fur Molekulare Genetik, Berlin, Germany

... Sequence analysis of the region located just upstream of coordinate 3643 using the BPROM (Softberry, Mount Kisco, NY) prediction program supported the latter hypothesis. It revealed the existence of an additional promoter sequence, here termed Pmob2 (Fig. ...


BMC Microbiology
2012, 12:268 doi:10.1186/1471-2180-12-268

Synergies between RNA degradation and trans-translation in Streptococcus pneumoniae: cross regulation and co-transcription of RNase R and SmpB

Ricardo N Moreira 1†, Susana Domingues 1†, Sandra C Viegas 1, Monica Amblar 2 and Cecilia M Arraiano 1*
1 Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157, Portugal 2 Unidad de Patologia Molecular del Neumococo, Centro Nacional de Microbiologia, and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III. Majadahonda, Madrid, 28220, Spain

...In silico predictions of putative promoters were performed using the BPROM SoftBerry software (http:/ / linux1.softberry.com/ berry.phtml?topic=bprom&group=progr ams&subgroup=gfindb webcite)...


PLoS ONE
7(8): e43444. doi:10.1371/journal.pone.0043444

Rhamnose-Inducible Gene Expression in Listeria monocytogenes

Lars Fieseler, Sibylle Schmitter , Justinas Teiserskas, Martin J. Loessner
Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania.

.. Putative -10 and -35 regions were identified by a promoter-finding algorithm (BPROM, http://linux1.softberry.com/berry.phtml). Cloning Procedures. Plasmid pPL2 was used for cloning and single copy insertion into a tRNA Arg gene via bacteriophage PSA site-specific integrase. ...


PLoS ONE
7(5): e36709. doi:10.1371/journal.pone.0036709

The mbo Operon Is Specific and Essential for Biosynthesis of Mangotoxin in Pseudomonas syringae

Carrion VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A
Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Malaga, Spain Laboratorio de Patologia Vegetal, ETS de Ingenieros Agronomos, Universidad Publica de Navarra, Pamplona, Spain

...The promoter (BPROM) and terminator (FindTerm and FoldRNA) prediction was performed using SoftBerry online programmes (http://www.softberry.com, Mount Kisco, NY, USA). ...


MicrobiologyOpen
Early View (Online Version of Record published before inclusion in an issue) DOI: 10.1002/mbo3.50

First insights into the syntrophic acetate-oxidizing bacteria – a genetic study

Bettina Muller *, Li Sun, Anna Schnurer
Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden

...BPROM, available online at http://www.softberry.com, was used as the promoter-prediction program....


AEM
Published ahead of print 14 September 2012, doi: 10.1128/AEM.01442-12

Phylogenetically novel LuxI/LuxR-type Quorum Sensing Systems Isolated Using a Metagenomic Approach

Nasuno et al.,
1Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan 2Graduate school of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan

... ausI from fosmid pN52. The G+C content in pN16 (56%) was lower than in pN52 (65%). 296 Promoter prediction software BPROM (Softberry, Mt. Kisco, NY, USA) identified 297 possible ?70 promoters in the upstream regions of both AHL-synthesizing enzyme genes, 298 ...


Plasmid
Volume 68, Issue 1, July 2012, Pages 1–12 DOI: 10.1016/j.plasmid.2012.01.009

Requirements for Borrelia burgdorferi plasmid maintenance

Kit Tilly, 1, , Claire Checroun1, 2, Patricia A. Rosa
Laboratory of Zoonotic Pathogens, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, United States

... 1C). The ability of this region to confer stable maintenance on a B. burgdorferi shuttle vector ( [Byram et al., 2004] and [Jewett et al., 2007a]) argues in favor of this hypothesis. Searching for a bacterial promoter using BPROM (Softberry, Inc., Mt. ...


J. Bacteriol.
May 2012 vol. 194 no. 9 2307-2320 DOI: .1128/JB.00142-12

Long-Range Transcriptional Control of an Operon Necessary for Virulence-Critical ESX-1 Secretion in Mycobacterium tuberculosis

Hunt et al.,
aDivision of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom bDepartment of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom

... A search for a possible promoter using Softberry BPROM (Mount Kisco, NY; a bacterial ? 70 prediction program) predicted a transcription start site at ?66 bp upstream of the translation start site in close agreement with the results described above. ...


J. Bacteriol.
October 2012 vol. 194 no. 19 5315-5324 DOI: 10.1128/JB.00984-12

Epoxide-Mediated CifR Repression of cif Gene Expression Utilizes Two Binding Sites in Pseudomonas aeruginosa

Ballok et al.,
aDepartment of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA bDepartment of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA

... Therefore, we utilized 5?RACE to map the start sites for the cifR gene and morB operon transcripts, as indicated in Fig. 4C. We next used the promoter prediction software, BPROM (SoftBerry), to identify the ?10 and ?35 sites for each sequence. As can be seen in Fig. ...


J. Bacteriol.
March 2012 vol. 194 no. 6 1523-1532 doi: 10.1128/JB.06104-11

Characterization of Escherichia colidinJ-yafQ Toxin-Antitoxin System Using Insights from Mutagenesis Data

Julija Armalyte, Milda Jurenaite, Gina Beinoraviciute, Justinas Teiserskas and Edita Suziedeliene
Department of Biochemistry and Biophysics, Faculty of Natural Sciences of Vilnius University, Vilnius, Lithuania

... The open arrowhead indicates free DNA; full arrowheads indicate DNA bound in complex with DinJ-YafQ(His) 6 . We have identified several palindromic sequences in the promoter region of dinJ-yafQ by sequence analysis (BPROM; Softberry, Inc., Mount Kisco, NY) (Fig. ...


Infect. Immun.
March 2012 vol. 80 no. 3 1037-1049 doi: 10.1128/IAI.05563-11

Pneumococcal Gene Complex Involved in Resistance to Extracellular Oxidative Stress

Andisi et al.,
aLaboratory of Molecular Bacteriology, Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands bMolecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, The Netherlands

...Therefore, we analyzed all intergenic regions by hand and with the BPROM software (Softberry, Mt. Kisco, NY); both methods...


BMC Genomics
2012, 13:550 doi:10.1186/1471-2164-13-550

Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

Patenge et al.,
1 Institute of Medical Microbiology and Hospital Hygiene, University of Rostock, Schillingallee 70, 18057, Rostock, Germany 2 Institute of Medical Microbiology, Genome Research, Justus-Liebig-University, Frankfurter Strasse 107, 35392, Giessen, Germany

... Terminators and promoters were predicted by TransTermHP [52] ( http://transterm.cbcb.umd. edu/tt/Streptococcus_pyogenes_NZ131.tt webcite) and BDGP Neural Network Promoter Prediction [53], and BProm ( http://www.SoftBerry.com webcite), respectively. ...


MPMI
Vol. 25, No. 1, 2012, pp. 119–128. DOI: 10.1094/ MPMI -07-11-0188

A Role for Bradyrhizobium japonicum ECF16 Sigma Factor EcfS in the Formation of a Functional Symbiosis with Soybean

S. B. Stockwell, 1 L. Reutimann, 2 and M. L. Guerinot 1
1 Biological Sciences Department, Dartmouth College, Hanover, NH 03755, U.S.A.; 2 ETH, Institute of Microbiology, Zurich, Switzerland

...Further promoter analysis was performed using motif searches (MEME Suite) (Bailey et al. 2009) and the virtual footprint algorithm (Softberry BPROM analysis tool) (Munch et al. 2005); ...


BMC Microbiology
2012, 12:173 doi:10.1186/1471-2180-12-173

Pyrosequencing-based analysis reveals a novel capsular gene cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil

Ramos et al.,
1 Laboratorio Nacional de Computacao Cientifica (LNCC), Petropolis, Rio de Janeiro, Brazil 2 Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil

... webcite. Prediction of promoters was performed using the in-house SABIA platform as well as the BPROM program (http://linux1.softberry.com webcite), which searches for promoters under the control of the sigma factor 70. ...


BMC Genomics
2012, 13:37 doi:10.1186/1471-2164-13-37

Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida

Hansen et al.,
1 Department of chemistry, Faculty of science and technology, University of Tromso, N-9037, Tromso, Norway 2 The Norwegian Structural Biology Centre, University of Tromso, N-9037, Tromso, Norway

... However, there is weak conservation among the predicted CRP sites in vibrios. The BPROM program (from http://www.softberry.com webcite) was used to predict -10 and -35 promoter sequences. Computational prediction of Spot42-pirin mRNA base-pairing. ...


PLoS ONE
7(3): e32977. doi:10.1371/journal.pone.0032977

Identification of the First Functional Toxin-Antitoxin System in Streptomyces

Laura Sevillano, Margarita Diaz, Yoshihiro Yamaguchi, Masayori Inouye, Ramon I. Santamaria
Instituto de Biologia Funcional y Genomica/Departamento de Microbiologia y Genetica, Consejo Superior de Investigaciones Cientificas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America

...BPROM software (http://linux1.softberry.com/berry.phtml) was used to search for conserved sequences in the putative promoter of the TA system....


Appl. Environ. Microbiol.
September 2012 vol. 78 no. 18 6568-6575 July 2012, doi: 10.1128/?AEM.01060-12

Mercury Resistance and Mercuric Reductase Activities and Expression among Chemotrophic Thermophilic Aquificae

Zachary Freedman a,b,*, Chengsheng Zhu a and Tamar Barkay a,b
aDepartment of Biochemistry and Microbiology bGraduate Program in Ecology and Evolution, Rutgers University, New Brunswick, New Jersey, USA

... (50). Of the 284 gene homologs available, 99 were selected for reconstruction; the selected homologs represented all major clusters in the MerA phylogeny. Putative promoter regions were determined using the BPROM tool (Softberry Inc., Mt. Kisco, NY). ...


Antimicrob. Agents Chemother.
January 2012 vol. 56 no. 1 565-568 doi: 10.1128/?AAC.00081-11

Description of a 2,683-Base-Pair Plasmid Containing qnrD in Two Providencia rettgeri Isolates

Thomas Guillard et al.,
aCHU Reims, Hopital Robert Debre, Laboratoire de Bacteriologie-Virologie-Hygiene, Reims, France bUFR Medecine, Universite Reims Champagne-Ardenne, Reims, France cUniversite Paris Diderot-Paris 7, Paris, France

... 2) (9): (i) an AT-rich region, (ii) iterons, (iii) three DnaA boxes, and (iv) two pairs of inverted repeats were identified using REPFIND (2). In addition, a putative promoter and transcription start site have been identified for Orf4 using BPROM (Softberry) and the promoter prediction ...


Extremophiles
Volume 16, Issue 3 , pp 363-376 DOI 10.1007/s00792-012-0435-2

Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon

Robert Lasek (1) Lukasz Dziewit (1) Dariusz Bartosik bartosik@biol.uw.edu.pl (1)
1. Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland

... 2010). Sequence alignments were per- formed using MUSCLE (Edgar 2004). Putative promoter sequences were predicted using BPROM (http://www. softberry.com/berry.html). Protein secondary structures were determined with the application of PredictProtein (Rost et al. ... Ïîõîæèå ñòàòüè Âñå âåðñèè ñòàòüè (5)


Enzyme and Microbial Technology
Volume 50, Issues 6–7, 10 May 2012, Pages 280–286 http://dx.doi.org/10.1016/j.enzmictec.2012.02.001

The direct repeat sequence upstream of Bacillus chitinase genes is cis-acting elements that negatively regulate heterologous expression in E. coli

Liang Xiao a, b, 1, Chuan Liu a, b, 1, Chi-chu Xie a, b, Jun Cai a, b, c, Yue-hua Chen a, b, c,
a Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China b Department of Microbiology, College of Life Sciences, Nankai University, Weijin Road 94, Tianjin 300071, PR China

... The chitinase genes were sequenced and the upstream regions were analyzed using online softwares REPFIND (http://zlab.bu.edu/repfind/form.html) and BPROM (http://linux1.softberry. com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). ...


Appl. Environ. Microbiol.
February 2012 vol. 78 no. 4 1298-1301 doi: 10.1128/?AEM.07278-11

Requirement for RNA Helicase CsdA for Growth of Yersinia pseudotuberculosis IP32953 at Low Temperatures

Eveliina Palonen et al.,
Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland

... An important role of CsdA at low temperatures was further confirmed by successful complementation of the csdA mutation. csdA and its putative native promoter, as predicted by BPROM (softberry, Inc., Mount Kisco, NY). were ...


Applied Microbiology and Biotechnology
Volume 93, Issue 4 , pp 1585-1599 DOI 10.1007/s00253-011-3684-6

Isolation of a strong promoter fragment from endophytic Enterobacter cloacae and verification of its promoter activity when its host strain colonizes banana plants

Yu Guang Wang et al.,
1. Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, People’s Republic of China 2. Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, People’s Republic of China

... Promoters were predicted with Neural Network Promoter Prediction (NNPP) v2.2 (http://www.fruitfly.org/ index.html) and BPROM of SoftBerry (http://linux1.softberry. com/berry.phtml). Identification of primary promoter functional fragments of complex cloned ...


Antimicrob. Agents Chemother.
doi: 10.1128/?AAC.00846-12 October 2012 vol. 56 no. 10 5171-5179

Reduced Expression of the rplU-rpmA Ribosomal Protein Operon in mexXY-Expressing Pan-Aminoglycoside-Resistant Mutants of Pseudomonas aeruginosa

Calvin Ho-Fung Lau a, Sebastien Fraud a, Marcus Jones b, Scott N. Peterson b and Keith Poole a
aDepartment of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada bThe J. Craig Venter Institute, Rockville, Maryland, USA

... Intriguingly, the mutation upstream of this operon occurred within the putative ?10 Pribnow box of the only predicted promoter for rplU-rpmA (SoftBerry BPROM promoter prediction software; SoftBerry, Inc., Mount Kisco, NY), 135 bp upstream of the rplU start codon (TTGCCT ...


BMC Microbiology
2012, 12:10 doi:10.1186/1471-2180-12-10

Characterisation of the mgo operon in Pseudomonas syringae pv. syringae UMAF0158 that is required for mangotoxin production

Eva Arrebola 1* et al.,
1 Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora" (IHSM-UMA-CSIC), Estacion Experimental La Mayora, Algarrobo-Costa, 29750 Malaga, Spain 2 Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Malaga, Spain

... The promoter prediction software BPROM (SoftBerry Inc.) was used to identify possible promoters in the putative mgo operon. ... The entire sequence of 118 bp was also analysed by FindTerm software (SoftBerry Inc.) to locate putative Rho-independent bacterial terminators. ...


BMC Microbiology
2012, 12:226 doi:10.1186/1471-2180-12-226

Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator

Valeria C Caballero et al.,
1 Program of Microbiology and Mycology, Institute of Biomedical Science (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile 2 Area of Biochemistry, Faculty of Dentistry, University of Chile, Santiago, Chile

... By mean of bioinformatics tools, including BPROM from the Softberry software package (http://linux1.softberry.com/berry.phtml), we identified those promoters in S. flexneri and included all three promoters in the constructs indicated in Figure 3A. ...


Front Microbiol.
2012; 3: 2. doi: 10.3389/fmicb.2012.00002

IncP-1e Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes

Holger Heuer et al.,
1Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kuhn-Institut, Braunschweig, Germany 2Department de Ciencias Biologicas, Universidad Adolfo Ibanez, Santiago, Chile

... to GenBank sequences. Additional searches for genes, operons, promoters, and terminators were done using FGENESB, BPROM, and FindTerm at www.softberry. com (Softberry, Mount Kisco, NY, USA). The sequence data ...


Microbiology.
2012 Jun;158(Pt 6):1581-92. doi: 10.1099/mic.0.055863-0. Epub 2012 Mar 1.

Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle.

Egan SA, Ward PN, Watson M, Field TR, Leigh JA.
The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Leicestershire, UK.

... Sequence analysis of the intergenic and promoter regions of the genes sub0144 (vru) and sub0145 (lbp) was performed using Artemis (Rutherford et al., 2000) and bprom from Softberry sequence analysis tools (http://linux1.softberry.com/berry.phtml?topic=bprom&group ...


AMB Express
2:41 DOI 10.1186/2191-0855-2-41

Revelation of the ability of sp. USM (JCM 15050) PHA synthase to polymerize 4-hydroxybutyrate monomer

Nyok-Sean Lau (1) Kumar Sudesh (1)
1. Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang, 11800, Malaysia

... Center for Biotechnology Information) and ClustalW Multiple Sequence Alignment program (Thompson et al., 1994). The potential promoter regions recognized by Sigma factor D (?D) were predicted using prediction of bacterial promoters (BPROM) provided by Softberry Inc. ...


Antimicrob. Agents Chemother.
April 2012 vol. 56 no. 4 1698-1702 doi: 10.1128/AAC.06199-11

Novel Plasmid and Its Variant Harboring both a blaNDM-1 Gene and Type IV Secretion System in Clinical Isolates of Acinetobacter lwoffii

Hongyan Hu et al.,
aDepartment of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces, Beijing, China bCAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

... constructing the phylogenetic tree. A multiple-sequence alignment was constructed using ClustalX version 1.8 (27). Promoter searches were performed by using Softberry's BPROM (Softberry Inc., Mt. Kisco, NY), PPP-Prokaryotic ...


Appl. Environ. Microbiol.
February 2012 vol. 78 no. 4 1228-1236

Identification of an Enzyme System for Daidzein-to-Equol Conversion in Slackia sp. Strain NATTS

Hirokazu Tsujia, Kaoru Moriyamaa, Koji Nomotoa and Hideyuki Akazab
aYakult Central Institute for Microbiological Research, Kunitachi, Tokyo, Japan bSystems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan

... For analysis of nucleotide sequences and amino acid sequences, DDBJ-BLAST (http://www.ddbj.nig.ac.jp/), BPROM (SoftBerry), GeneMark version 2.5 (http://opal.biology.gatech. edu/GeneMark/), FindTerm (SoftBerry), and PSORT (http://psort.ims.u-tokyo.ac.jp/) were used. ...


Applied Biochemistry and Biotechnology
September 2012 Online ISSN 1559-0291 DOI 10.1007/s12010-012-9889-z

Characterization of a Glycoside Hydrolase Family 1 b-Galactosidase from Hot Spring Metagenome with Transglycosylation Activity

Richa Gupta, Tanvi Govil, Neena Capalash, Prince Sharma
1. Department of Biotechnology, Panjab University, Chandigarh, 160014, India 2. Department of Microbiology, Panjab University, Chandigarh, 160014, India

... Motifs in the considered sequences were scanned using PROSITE [19]. N-terminal signal peptide analysis was done using Signal IP version 3.0 program [20], and the promoter was located using SoftBerry BPROM tool (http://www.soft berry.com/berry.html). ...


Antimicrob. Agents Chemother.
June 2012 vol. 56 no. 6 3392-3394

Functional Characterization of a Cassette-Specific Promoter in the Class 1 Integron-Associated qnrVC1 Gene

Erica Lourenco da Fonseca and Ana Carolina Paulo Vicente
Laboratorio de Genetica Molecular de Microrganismos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil

... presence of internal cassette-specific promoters of aadA2 and qnrVC1 using four promoter prediction programs: Neural Network for Promoter Prediction (NNPP) version 2.2 (Berkeley Drosophila Genome Project, http://www.fruitfly.org/index.html), BPROM (SoftBerry, http://linux1 ...


Journal of Biomedical Science and Engineering
Year: 2011 Volume: 04 Issue: 01 Pages: 70-75 DOI: 10.4236/jbise.2011.41009

Analysis of the arginine biosynthetic gene cluster argCJBDFR of Corynebacterium crenatum

Haitao Jiao, Yong Yuan, Yonghua Xiong, Xuelan Chen

... The sequence data were compiled, aligned and ana- lyzed using Lasergene software (DNASTAR), Soft- berry's BPROM (www.softberry.com) and RNAshapes WebServices (BiBiServ) et al. 3. RESULTS AND DISCUSSION 3.1. ...


Biologia
2011, vol. 66, no4, pp. 565-573

The role of TerW protein in the tellurite resistance of uropathogenic Escherichia coli

Valkovicova et al.,
(1) Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, SK-84215, Bratislava, Slovakia

... and cloning of a potential promoter se- quence The potential promoter rich region (PPRR) of the ter operon was determined with the help of the Neural Network Promoter Prediction software (http://www.fruitfly.org/ seq tools/promoter.html) and Softberry-BPROM software (http ...


Antonie van Leeuwenhoek
Volume 99, Issue 2 , pp 409-416 DOI: 10.1007/s10482-010-9476-7

Characterization of transcription within sdr region of Staphylococcus aureus

Izabela Sitkiewicz, Ireneusz Babiak, Waleria Hryniewicz
1. Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chelmska 30/34, Warszawa, Poland 2. Department of Orthopedics and Traumatology of Locomotory System, Medical University of Warsaw, Warsaw, Poland

... The presence of putative promoters and transcrip- tional organization of the sdr region was detected using the BPROM and FGENESB algorithms (www. softberry.com) based on region 611262 bp–623152 bp (GeneBank number CP000730.1) of the S. aureus subsp. ...


FEMS Microbiology Letters
314: 18–24. doi: 10.1111/j.1574-6968.2010.02132.x

ISPsa2, the first mobile genetic element to be described and characterized in the bacterial facultative intracellular pathogen Piscirickettsia salmonis.

Marshall, S. H., Henriquez, V., Gomez, F. A. and Cardenas, C.
1 Laboratorio de Genetica e Inmunologia Molecular, Instituto de Biologia, Facultad de Ciencias, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile 2 NBC, Nucleo de Biotecnologia Curauma, Curauma, Valparaiso, Chile

... sequencing by Macrogen Inc. (Korea). Sequence analysis. The DNA sequence data were analyzed with softberry server software (http://linux1.softberry.com/berry.phtml) using the FgenesB and Bprom algorithms. FgenesB is a suite ...


J. Antimicrob. Chemother.
(2011) 66 (4): 797-801. doi: 10.1093/jac/dkr011

Pc promoter from class 2 integrons and the cassette transcription pattern it evokes

Erica Lourenco da Fonseca*, Fernanda dos Santos Freitas and Ana Carolina Paulo Vicente
Laboratorio de Genetica Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil

... The attI2 site sequence and the intI2* gene were submitted to four promoter predictor programs: Neural Network for Promoter Prediction version 2.2 (Berkeley Drosophila Genome Project, http://www.fruitfly.org/index.html); BPROM (SoftBerry, http://linux1.softberry.com/berry.phtml ...


J. Antimicrob. Chemother.
(2011) 66 (5): 1005-1012. DOI: 10.1093/jac/dkr041

Variation in the genetic environments of blaCTX-M-15 in Escherichia coli from the faeces of travellers returning to the United Kingdom

Dhanji et al.,
1Antibiotic Resistance Monitoring and Reference Laboratory, Health Protection Agency Microbiology Services – Colindale, 61 Colindale Avenue, London NW9 5EQ, UK 2North West London NHS Trust, Northwick Park Hospital, London HA1 3UJ, UK

... DNA sequences that did not contain published bla CTX-M promoters were analysed with 'SoftBerry BPROM' software. 23. A potential alternative promoter region (promoter X) was investigated by cloning and northern blotting. ...


BMC Genomics
2011, 12:282 doi:10.1186/1471-2164-12-282

Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

Oakley et al.,
1 Poultry Microbiological Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, Athens, GA 30605, USA 2 Department of Infectious Diseases & Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30306, USA

... The transcriptional regulation of these genes in our phages remains unknown, but searches for transcriptional promoters and terminators using BPROM (Softberry, Inc., Mount Kisco, NY, USA; http://linux1.softberry.com/berry.phtml webcite) and TransTerm (http://nbc3.biologie.uni ...


Biochem. J.
(2011) 433 (107–117) (Printed in Great Britain) doi:10.1042/BJ20101186

Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression

Montero et al.,
Agrobioteknologiako Instituta, Nafarroako Unibertsitate Publikoa and Consejo Superior de Investigaciones Cientificas, Mutiloako etorbidea zenbaki gabe, 31192 Mutiloabeti, Nafarroa, Spain

... Protein content was measured by the Bradford method using a Bio-Rad prepared reagent. Computer analyses. Promoters were predicted using the BPROM program (SoftBerry, http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). ...


Molecular Microbiology
(2011) 79: 1602–1614. doi: 10.1111/j.1365-2958.2011.07543.x

tRNA accumulation and suppression of the bldA phenotype during development in Streptomyces coelicolor.

Pettersson, B. M. F. and Kirsebom, L. A.
Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden.

...The Softberry BPROM promoter prediction software (http://linux1.softberry.com/berry.phtml) was used to predict the tRNAHisGUG and the known tRNALeuUAA transcription start sites, while the tRNALeuCAA transcription start site was manually predicted on the basis of similarity to Escherichia coli?70 promoters....


Antimicrob. Agents Chemother.
December 2011 vol. 55 no. 12 5850-5860 doi: 10.1128/AAC.00498-11

Fluoroquinolone Efflux in Streptococcus suis Is Mediated by SatAB and Not by SmrA

Escudero et al.,
1Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain 2Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain

... Promoter sequence analysis was performed with Bprom (Softberry, Inc., Mount Kisco, NY). Protein modeling was done using Phyre server (23) and illustrated using the PyMOL molecular graphics system (version 1.3; Schrodinger, LLC). ...


Metallomics,
2011,3, 1009-1018 DOI: 10.1039/C1MT00127B

A novel nickel responsive MerR-like regulator, NimR, from Haemophilus influenzae

Kidd et al.,
School of Molecular and Biomedical Science, The University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia.

... Our in silico analysis identified the promoter regions for each of these using BPROM (Softberry: www.softberry.com) and the likely MerR-like binding site .19 HI1623 is annotated as CadR, indicating that it is a cadmium responsive protein . ...


Antimicrob. Agents Chemother.
January 2011 vol. 55 no. 1 361-363 doi: 10.1128/AAC.01672-09

A Novel Insertion Sequence, ISAba10, Inserted into ISAba1 Adjacent to the blaOXA-23 Gene and Disrupting the Outer Membrane Protein Gene carO in Acinetobacter baumannii

Lee et al.,
1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-gu, Seoul 120-752, South Korea 2Korean Institute of Tuberculosis, 14 Woomyun-dong, Seocho-gu, Seoul 137-900, South Korea

... additional promoter sequences to the bla OXA-23 gene. Analyses using the online tool BPROM (Softberry, Inc., Mount Kisco, NY) suggested the presence of a putative promoter within the ISAba10 element (Fig. 1). View this table ...


Virology Journal
2011, 8:142 http://www.virologyj.com/content/8/1/142

Complete genome sequence of the lytic Pseudomonas fluorescens phage fjIBB-PF7A

Sillankorva et al.,
IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal

... proteins were determined using the ExPASy Compute pI/Mw tool http://au.expasy.org/ tools/pi_tool.html. Promoter predictions were made using promoter predictor http://www.fruitfly. org/seq_- tools/promoter.html, PHIRE 1.0 [28] and BPROM http:// linux1.softberry.com/berry.phtml ... ...Terminators were predicted using FindTerm http://linux1.softberry. com/berry.phtml?topic=findterm&group=programs&subgroup=gfindb ...


Antimicrob. Agents Chemother.
April 2011 vol. 55 no. 4 1460-1469 doi: 10.1128/AAC.01094-10

Role of VltAB, an ABC Transporter Complex, in Viologen Tolerance in Streptococcus mutans

Saswati Biswas and Indranil Biswas
Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Centre, Kansas City, Kansas 66160

... In silico analysis by BPROM software (Softberry, Inc.) indicates that this region contains a weak promoter-like sequence (?10 box [TATATT] at position 362), indicating that vltAB may be transcribed separately from SMU.902. ...


Antimicrob. Agents Chemother
December 2011 vol. 55 no. 12 5942-5945 doi: 10.1128/AAC.05142-11

Quinolone Induction of qnrVS1 in Vibrio splendidus and Plasmid-Carried qnrS1 in Escherichia coli, a Mechanism Independent of the SOS System

Okumura et al.,
1Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 2 Biological Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan

... host (Table 3), we amplified by PCR (primer pairs in Table 4) and cloned a 1,011-bp BamHI-EcoRI fragment containing qnrVS1, 258 bp of upstream sequence, including the potential native promoter sequence (bacterial promoter prediction program from Softberry), and 85 bp of ...


Veterinary Microbiology
Volume 153, Issues 3–4, 15 December 2011, Pages 403–406 DOI: 10.1016/j.vetmic.2011.05.050

The cps locus of Streptococcus suis serotype 16: Development of a serotype-specific PCR assay

Kaicheng Wang a, b, c, Weixing Fan c, Henk Wisselink d, Chengping Lu a, b
a Key Lab Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China b College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China

... Vector NTI. Putative promoter and terminator sequences were predicted by BPROM and FindTerm program on http://www.softberry.ru/berry.phtml, respectively. 2.4. Screening of serotype-specific gene. Cross-hybridization experiments ...


FEMS Microbiology Letters
(2011), 323: 97–104. doi: 10.1111/j.1574-6968.2011.02365.x

The copper responding surfaceome of Methylococccus capsulatus Bath

Karlsen, O. A., Larsen, O., Jensen, H. B.
1Department of Molecular Biology, University of Bergen, Norway 2UNI Research, Bergen, Norway

... b Predicted upstream promoter using bprom (http://linux1.softberry.com/all.htm) or promscan (http://molbiol-tools.ca/promscan/) promotor prediction software. c (Y, yes) or (N, no) indicates if the encoding gene is part of an operon structure. ...


Infect. Immun.
January 2011 vol. 79 no. 1 342-352 doi: 10.1128/IAI.00736-10

Characterization of a Staphylococcus aureus Surface Virulence Factor That Promotes Resistance to Oxidative Killing and Infectious Endocarditis

Malachowa et al.,
1Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, Idaho 83844 2Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland

... The BPROM program (Softberry, Inc., Mount Kisco, NY) was used to predict bacterial promoter. DNA isolation.Genomic DNA was isolated by using Genomic DNA Prep Plus kits (A&A Biotechnology, Gdynia, Poland) facilitated by a method to promote S. aureus lysis (41). ...


Applied Microbiology and Biotechnology
Volume 90, Issue 1 , pp 159-172 DOI: 10.1007/s00253-010-3028-y

Discovery and characterization of d-phenylserine deaminase from Arthrobacter sp. TKS1

Muramatsu et al.,
1. Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502, Japan 2. Graduate School of Integrated Arts and Sciences, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502, Japan

... Institute (Finn et al. 2008). The prediction of the bacterial promoter was performed with the BPROM software at SoftBerry (http:// linux1.softberry.com/berry.phtml). Nucleotide sequence accession number The nucleotide sequence ...


World Journal of Microbiology and Biotechnology
Volume 27, Issue 2 , pp 431-441 DOI: 10.1007/s11274-010-0475-7

Gene cloning, expression and characterization of a cold-adapted lipase from a psychrophilic deep-sea bacterium Psychrobacter sp. C18

Ruipeng Chen, Lizhong Guo, Hongyue Dang
1. College of Life Sciences, Qingdao Agricultural University, 266109, Qingdao, China 2. State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 266555, Qingdao, China

... version 2.0; Larkin et al. 2007). The upstream regulatory sequence signatures of the putative lipase genes were analyzed using the online BPROM program (http://linux1. softberry. com/berry.phtml?topic=index&group=programs&subgroup ...


International Journal of Food Microbiology
Volume 151, Issue 2, 2 December 2011, Pages 171–181 DOI: 10.1016/j.ijfoodmicro.2011.08.019

Characterization of Streptococcus thermophilus two-component systems: In silico analysis, functional analysis and expression of response regulator genes in pure or mixed culture with its yogurt partner, Lactobacillus delbrueckii subsp. bulgaricus

Thevenard et al.,
a INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France b AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France

... Presence of putative promoters, terminators and operons was evaluated using BPROM (http://linux1.softberry.com/berry.phtml) and BDGP (http://www.fruitfly.org/seq_tools/promoter. html), FINDTERM (http://linux1.softberry.com/berry.phtml), TransTermHP (http://transterm.cbcb ...


Antimicrob. Agents Chemother.
January 2011 vol. 55 no. 1 118-123 doi: 10.1128/AAC.01062-10

Metallo-b-Lactamase Production by Pseudomonas otitidis: a Species-Related Trait

Thaller et al.,
1Dipartimento di Biologia, Universita di Roma “Tor Vergata,” I-00133 Rome, Italy 2Dipartimento di Biologia Molecolare, Sezione di Microbiologia, Universita di Siena, I-53100 Siena, Italy

... phylogenetic trees. Signal peptide cleavage site was predicted using SignalP (version 3.0). Putative promoter sequences were detected using Bprom software (Softberry, Inc., Mount Kisco, NY). Nucleotide sequence accession ...


BioData Mining
2011, 4:22 http://www.biodatamining.org/content/4/1/22

Detection of putative new mutacins by bioinformatic analysis using available web tools

Guillaume G Nicolas
Departement de Biochimie Microbiologie et Bioinformatique, Faculte des Sciences et Genie, Universite Laval, Quebec (Quebec), G1K7P4, Canada

... Upstream genomic coding sequence was analyse to detect putative promoter regions and transcription factor binding sites using the bacterial promoter recognition program BPROM (Softberry inc.) (Figure 2). Many putative mutacin-encoding genes have been previously ...


Appl. Environ. Microbiol.
January 2011 vol. 77 no. 1 281-290 doi: 10.1128/AEM.01403-10

Ethanolamine Utilization Contributes to Proliferation of Salmonella enterica Serovar Typhimurium in Food and in Nematodes

Shabarinath Srikumar and Thilo M. Fuchs
Zentralinstitut fur Ernahrungs- und Lebensmittelforschung (ZIEL), Abteilung Mikrobiologie, Technische Universitat Munchen, Weihenstephaner Berg 3, D-85354 Freising, Germany

... The home pages for NCBI and Microbes Online were used to determinate the distribution of the pdu and eut clusters in different serotypes of S. enterica. Promoter sequences located upstream of the genes identified were predicted with BPROM (Softberry). ...


J. Bacteriol.
October 2011 vol. 193 no. 19 5300-5313 doi: 10.1128/JB.05287-11

Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia

Jason J. Gill et al.,
1Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128 2Center for Phage Technology, Texas A&M University, College Station, Texas 77843-2128

... Protein sequences were compared to the NCBI protein database by using BLASTp (9); tRNA genes were detected with tRNAscan (68); rho-independent terminators were detected with TransTerm HP (37); promoters were detected using BPROM (Softberry). ...


Infection, Genetics and Evolution
Volume 11, Issue 6, August 2011, Pages 1352–1360 DOI: 10.1016/j.meegid.2011.04.029,

Pseudomonas entomophila and Pseudomonas mendocina: Potential models for studying the bacterial type VI secretion system

Panagiotis F. Sarris a, b, Effie V. Scoulica b
a Department of Biology, University of Crete, P.O. Box 2208, 71409 Heraklion, Greece b Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine, University of Crete, 71409 Heraklion, Greece

.. Thereby, in order to identify T6SS gene clusters potentially controlled by sigma factors we performed a survey using the BPROM algorithm (www.softberry.com). ... The sequences were used for analysis by the BPROM algorithm (www.softberry.com) (Table S1). ...


Appl. Environ. Microbiol.
March 2011 vol. 77 no. 5 1608-1618 doi: 10.1128/AEM.01862-10

Identification and Characterization of Novel and Potent Transcription Promoters of Francisella tularensis

Zaide et al.,
Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, P.O. Box 19, Ness Ziona 74100, Israel

... Computational analysis of promoter elements.The sequences of all the unique promoter clone DNA inserts were subjected to regulatory element analysis using the BPROM bacterial promoter prediction program (Softberry). ...


Antimicrob. Agents Chemother.
February 2011 vol. 55 no. 2 917-920 doi: 10.1128/AAC.00491-10

SAba825, a Functional Insertion Sequence Modulating Genomic Plasticity and blaOXA-58 Expression in Acinetobacter baumannii

Pablo Ravasi, Adriana S. Limansky, Ramiro E. Rodriguez, Alejandro M. Viale and Maria A. Mussi
Instituto de Biologia Molecular y Celular de Rosario (IBR, CONICET) and Departamento de Microbiologia, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina

... The ?35 and ?10 motifs inferred for each of the different promoters are boxed, and the transcription initiation site (G in bold) resulting from the hybrid promoter (as determined by 5? RACE-PCR) is indicated by +1. Promoter prediction was done using BPROM (SoftBerry). ...


BMC Genomics
2011, 12:198 doi:10.1186/1471-2164-12-198

Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny

Rolf Lood* and Mattias Collin
Department of Clinical Sciences, Division of Infection Medicine, BMC-B14, Lund University, SE-221 84 Lund, Sweden

... The genome of PAD20, PAS50 and PA6 were screened for putative sigma70- promoters using SAK and BPROM (Softberry, Inc.). ... Terminator structures were identified using FindTerm (Softberry, Inc.) and EMBOSS Explorer [43]. ...


J Proteomics Bioinform
4: 179-183. doi:10.4172/jpb.1000187

Bacillus clausii and Bacillus halodurans lack GlnR but Possess Two Paralogs of glnA

Farazmand A, Yakhchali B, Shariati P, Ofoghi H
1Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), 15815-3538, Tehran, Iran 2Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965-161 Tehran, Iran

...the bacterial promoter prediction program, BPROM (www.softberry.com/berry.html) was used. ...


PLoS ONE
(2011) 6(3): e18197. doi:10.1371/journal.pone.0018197

Identification of a Cryptic Prokaryotic Promoter within the cDNA Encoding the 5? End of Dengue Virus RNA Genome.

Li D, Aaskov J, Lott WB
Infectious Diseases Program, Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology, Brisbane, Australia

... The BPROM promoter prediction program (SoftBerry, Mount Krisco, NY) identified potential ?35 and ?10 bacterial promoter elements at DENV2 cDNA nt positions 53 (TCAACG) and 72 (TTTTTAAT), respectively, which share sequence homology with the wild type E. coli ...


J. Bacteriol.
December 2011 vol. 193 no. 24 6824-6833 doi: 10.1128/JB.05492-11

Mycobacterium smegmatis RoxY Is a Repressor of oxyS and Contributes to Resistance to Oxidative Stress and Bactericidal Ubiquitin-Derived Peptides

Aaron Daugherty, Katelyn M. Powers, Melissa S. Standley, Cathy S. Kim and Georgiana E. Purdy
Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239

... (D) A diagram of the roxY promoter as well as the homologous synthetic oligonucleotides. The bent arrow denotes the putative transcription start site and the black boxes the putative ?10 and ?35 regions, respectively, as predicted by Bprom (Softberry, Inc.). ...


BMC Microbiology
2011, 11:259 doi:10.1186/1471-2180-11-259

The small heat shock proteins from Acidithiobacillus ferrooxidans: gene expression, phylogenetic analysis, and structural modeling

Ribeiro et al.,
1 Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas - UNICAMP, Candido Rondon Avenue 400, 13083-875 - Campinas, SP, Brazil 2 National Biosciences Laboratory (LNBio), National Laboratory of Energy and Materials Research (CNPEM), Giuseppe Maximo Scolfaro Street 10000, 13083-970 - Campinas, SP, Brazil

... The alignment was edited with the GeneDoc program [15]. Prediction of the transcription start site was performed with BPROM software (Softberry, Inc.). A widely accepted theoretical informational approach was adopted to identify potential ? 32 sites [16,17]. ...


Applied Microbiology and Biotechnology
Volume 90, Issue 6 , pp 1963-1971 DOI: 10.1007/s00253-011-3203-9

Characterization of a gene cluster and its putative promoter region for violacein biosynthesis in Pseudoalteromonas sp. 520P1

Xi Zhang, Keiichi Enomoto
1. Department of Environmental Systems Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan

... 2008), was obtained by PCR using primers 520P1-before-vioA-Fw2 and 520P1-vioA- Rv1. Promoter prediction was performed with BPROM software (SoftBerry, Mount Kisco, NY, USA). Cloning and expression of the violacein gene cluster ...


Appl. Environ. Microbiol.
July 2011 vol. 77 no. 14 4802-4810 doi: 10.1128/AEM.05149-11

Cholesterol Degradation by Gordonia cholesterolivorans

O. Drzyzga 1, L. Fernandez de las Heras 1, V. Morales 2, J. M. Navarro Llorens 1 and J. Perera 1
1Departamento de Bioquimica y Biologia Molecular I, Universidad Complutense de Madrid, 28040 Madrid, Spain 2Departamento de Biologia Medioambiental, Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain

... Putative promoters were analyzed by using the Neural Network Promoter Prediction (NNPP), Promscan, and BPROM programs (http://www.fruitfly.org/seq_tools/promoter.html, http://molbiol-tools.ca/promscan/, and http://linux1.softberry.com/berry.phtml, respectively), in ...


Iranian Journal of Microbiology
2011;3(1) : 13-20

The influence of riboflavin and nicotinic acid on Shigella sonnei colony conversion

Dr. Bagher Yakhchali
National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e-Pajoohesh, km 15, Tehran-Karaj Highway, Tehran, Iran.

... CP000038) and analyzed by “Virtual Footprint Online Software” for the presence of OxyR binding site (19) and by online software “BPROM - Prediction of bacterial promoters of Softberry” for promoter prediction. All primers were analyzed by in silico simulation of PCR (20). ...


J. Bacteriol.
February 2011 vol. 193 no. 3 611-619 doi: 10.1128/JB.01185-10

The Three Vibrio cholerae Chromosome II-Encoded ParE Toxins Degrade Chromosome I following Loss of Chromosome II

Jie Yuan ,2,3, Yoshiharu Yamaichi 1, and Matthew K. Waldor 1,2
1Channing Laboratory, Brigham and Women's Hospital and Department of Microbiology and Molecular Genetics, Harvard Medical School 2HHMI

... However, bioinformatic analyses of parDE1/3 and parDE2 using BPROM (Softberry, Inc., Mount Kisco, NY) suggested that, in addition to the expected ParD promoters, P parD1 and P parD2 , the parE genes might have their own promoters, P parE1 and P parE2 . ...


Proc. R. Soc.
January 2011 vol. 278 no. 1702 115-121 DOI: 10.1098/rspb.2010.1304

Sources of variation in dietary requirements in an obligate nutritional symbiosis

Kevin J. Vogel* and Nancy A. Moran
Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA

... Of the 87 single nucleotide changes, six were located in the region immediately upstream of a coding region, although none was found in a ?10/?35 promoter region as identified by BPROM (http://www.softberry.com), suggesting that these mutations have no effect on gene ...


Front Microbiol.
2011; 2: 147. DOI: 10.3389/fmicb.2011.00147

Regulation of Multiple Carbon Monoxide Consumption Pathways in Anaerobic Bacteria

Techtmann et al.,
1Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, USA 2Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA

... These sequences were run through the bprom program (http://softberry.com) to predict the putative -10 and -35 sites. From this prediction, primers were designed to create a product that started at the putative -150 site and stretched to start codon. ...


J. Bacteriol.
May 2011 vol. 193 no. 9 2158-2167 DOI: 10.1128/JB.00029-11

Regulation of Type VI Secretion Gene Clusters by ?54 and Cognate Enhancer Binding Proteins

Christophe S. Bernard, Yannick R. Brunet, Marthe Gavioli, Roland Lloubes and Eric Cascales
Laboratoire d'Ingenierie des Systemes Macromoleculaires Institut de Microbiologie de la Mediterranee Aix-Marseille Universite CNRS—UPR9027, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France

... RESULTS. Identification of ? 54 binding boxes.To identify T6SS gene clusters potentially controlled by ? 54 , we performed a survey using the BProm algorithm (SoftBerry). The putative ? 54 -dependent T6SS promoter list includes ...


AEM
Published ahead of print 18 November 2011, doi: 10.1128/AEM.07480-11

Genomic and functional analysis of the IncP-1b plasmids pWDL7::rfp and pNB8c explains their role in chloroaniline catabolism

Krol et al.,
1Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, PO Box 443051, Moscow, ID 83844-3051,U.S.A. 2Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A.

... with identity scoring by ClustalW. The pdca promoter region was analyzed using BPROM 154 (Softberry Inc., Mount Kisco, NY). 155 To infer the phylogenetic relationships of various IncP-1 plasmids, the deduced amino 156 ...


Archives of Microbiology
Volume 193, Issue 9 , pp 641-650 DOI: 10.1007/s00203-011-0705-x

Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400

Patrauchan et al.,
1. Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada 2. Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 LSE, Stillwater, OK, 74075, USA

... 2001) was used to search for conserved domains and motifs and to validate predicted gene function. Potential promoter regions were calculated using BPROM software (www.softberry.com) for paa genes using the gene sequence with a 100-bp upstream fragment. ...


Microbiological Research
Volume 166, Issue 5, 20 July 2011, Pages 403–418 DOI: 10.1016/j.micres.2010.05.003

ChoG is the main inducible extracellular cholesterol oxidase of Rhodococcus sp. strain CECT3014

Fernandez de Las Heras L, Mascaraque V, Garcia Fernandez E, Navarro-Llorens JM, Perera J, Drzyzga O.
a Departamento de Bioquimica y Biologia Molecular I, Universidad Complutense de Madrid, 28040 Madrid, Spain b Departamento de Biologia Medioambiental, Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, 28040 Madrid, Spain

... Putative prokaryotic promoters were analysed by the Neural Network Promoter Prediction (NNPP) server (http://www.fruitfly.org/seq_tools/promoter.html) (Reese et al., 1996), Promscan server (http://molbiol-tools.ca/promscan/) and Bprom server (http://linux1.softberry.com/berry ...


J. Bacteriol.
May 2011 vol. 193 no. 9 2312-2321 DOI: 10.1128/JB.01355-10

Partial Functional Replacement of CymA by SirCD in Shewanella oneidensis MR-1

Carmen D. Cordova 2, Marcus F. R. Schicklberger 2,#, Yang Yu 2 and Alfred M. Spormann 1,2
1 Departments of Chemical Engineering 2 Civil & Environmental Engineering, Stanford University, Stanford, California

... coli based) (http://www.prodoric.de/vfp/) (29). The BPROM bacterial promoter predictor was used to identify entire (?35/?10) putative promoter regions (SoftBerry, Mt. Kisco, NY). E. coli-based predictions were deemed suitable ...


Nucl. Acids Res.
(2011) 39 (13): 5622-5632. doi: 10.1093/nar/gkr166

Antisense RNA associated with biological regulation of a restriction–modification system

Iwona Mruk 1,2, Yaoping Liu 2,3, Liying Ge 2 and Ichizo Kobayashi 2,3,4
1Department of Microbiology, University of Gdansk, Kladki 24, Gdansk, 80-822, Poland, 2Department of Medical Genome Sciences, Graduate School of Frontier Sciences

... to agar plates. Bioinformatic analyses. In silico promoter prediction and terminator prediction were performed using the BPROM and FindTerm software, respectively (http://www.softberry.com/all.htm). RNA secondary structure ...


Bioscience, Biotechnology, and Biochemistry
Vol. 75 (2011) No. 5 P 944-952 DOI: 10.1271/bbb.100921

The Genome of Bacillus subtilis Phage SP10: A Comparative Analysis with Phage SPO1

YEE et al.,
1) Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University 2) Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture 3) Department of Bioscience, Tokyo University of Agriculture

... 2. The promoters recognized by the RNA polymerase holoenzyme containing sigma-A and the & independent terminators were predicted using the BPROM and the FindTerm program respectively (http://www.softberry.ru/ berry.phtml). They are shown in Fig. ...


PLoS Genet
(2011), 7(11): e1002349. doi:10.1371/journal.pgen.1002349

Attenuation of the Sensing Capabilities of PhoQ in Transition to Obligate Insect–Bacterial Association.

Pontes MH, Smith KL, De Vooght L, Van Den Abbeele J, Dale C
Department of Biology, University of Utah, Salt Lake City, Utah, United States of America Department of Biological Sciences, Institute of Tropical Medicine, Antwerp, Belgium

... PhoP boxes (inverted text) and putative ribosomal binding site (bold) were identified by visual inspection of the promoter regions. Putative -35 and -10 regions (underlined) were identified using the online BPROM tool (SoftBerry, Inc.). doi:10.1371/journal.pgen.1002349.g004. ...


Archives of Microbiology
Volume 193, Issue 4 , pp 263-274 DOI: 10.1007/s00203-010-0669-2

Two promoters and two translation start sites control the expression of the Shigella flexneri outer membrane protease IcsP

Hensley et al.,
1. School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV, 89154-4004, USA 2. Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA

... To identify putative promoter sequences, the intergenic region upstream of icsP was entered into the BPROM program for prediction of promoters regulated by the r70 subunit of RNA polymerase (http://www.linux1. softberry.com). ...


Molecular Microbiology
(2011), 80: 1260–1275. doi: 10.1111/j.1365-2958.2011.07641.x

Antagonistic regulation of dgkA and plsB genes of phospholipid synthesis by multiple stress responses in Escherichia coli.

Wahl, A., My, L., Dumoulin, R., Sturgis, J. N. and Bouveret, E.
LISM, CNRS, Aix-Marseille University, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

... ?E-dependent promoter. We ran a search on the dgkA-plsB intergenic sequence for a putative promoter using a set of bioinformatic servers and got a low hit using BPROM (http://www.softberry.com/berry.phtml). A +1 transcription ...


Journal of Bioscience and Bioengineering
Volume 112, Issue 5, November 2011, Pages 422–431 DOI: 10.1016/j.jbiosc.2011.07.020

Molecular cloning and characterization of two inducible NAD+-adh genes encoding NAD+-dependent alcohol dehydrogenases from Acetobacter pasteurianus SKU1108

Uraiwan Masud 1, Kazunobu Matsushita 2, Gunjana Theeragool 1, 3
1 Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand, 2 Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753–8515, Japan,

... Based on the E. coli sigma 70 promoter recognition program (BPROM tool of Softberry), the predicted ? 35 and ? 10 sequences of sigma 70, TTTATT and TGTTTGTAAAAT, were located from the 961st to 966th and 976th to 987th nucleotide (nt) of the adhI gene, respectively. ...


J. Bacteriol.
May 2011 vol. 193 no. 10 2575-2586 doi: 10.1128/JB.00217-11

Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B12 Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis

Kris Ann Baker and Marta Perego
The Scripps Research Institute, Department of Molecular and Experimental Medicine, La Jolla, California 92037

... In order to determine whether the promoter activity in the eutT-eutG intergenic region was upstream or downstream from the riboswitch, the sequence of the eutT-eutG intergenic region was analyzed with the Softberry BPROM program. ...


J. Bacteriol.
May 2011 vol. 193 no. 10 2536-2548 doi: 10.1128/JB.00815-10

Identification of ArgP and Lrp as Transcriptional Regulators of lysP, the Gene Encoding the Specific Lysine Permease of Escherichia coli

Jimena Ruiz ‡, Ina Haneburger and Kirsten Jung
Ludwig-Maximilians-Universitat Munchen, Munich Center for integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany

... Predicted ?35 and ?10 promoter motifs (BProm; http://linux1.softberry.com/berry.phtml? topic=bprom&group=help&subgroup=gfindb) and the start of transcription (position +1) previously identified by primer extension analysis (32) are indicated. ...


Antimicrob. Agents Chemother.
April 2011 vol. 55 no. 4 1638-1649 doi: 10.1128/AAC.01366-10

Mutational Analysis of the Thienamycin Biosynthetic Gene Cluster from Streptomyces cattleya

Rodriguez et al.,
Departamento de Biologia Funcional e Instituto Universitario de Oncologia del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain

... operon thnKJI. Other putative promoter sequences have also been identified for the ThnI-independent genes (Fig. 1C) by the use of the BPROM bacterial promoter prediction server (Softberry Inc., Mount Kisco, NY). Upstream of ...


J. Bacteriol.
August 2011 vol. 193 no. 15 3988-3997 doi: 10.1128/JB.05186-11

A Sulfite Respiration Pathway from Thermus thermophilus and the Key Role of Newly Identified Cytochrome c550

Robin et al.,
1Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland 2Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche c/o Dipartimento di Scienze Biochimiche, Sapienza Universita di Roma Piazzale Aldo Moro 5, I-00185 Rome, Italy

... are yet to be elucidated. A unique promoter upstream of TTHA1325 and a unique terminator region downstream of TTHA1327 were identified using BPROM and FindTerm (Softberry), respectively. Those findings showed that ...


BMC Genomics
2011, 12:479 doi:10.1186/1471-2164-12-479

Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq

Yi Wang 1,2, Xiangzhen Li 3, Yuejian Mao 3 and Hans P Blaschek 2,4,5
1 Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA 2 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

... A prediction of the promoters for primary sigma factors for all the putative HKGs was carried out using BPROM (http://linux1.softberry.com/berry.phtml webcite). ...


FEMS Microbiology Letters
(2011), 325: 56–63. doi: 10.1111/j.1574-6968.2011.02416.x

Genetic analysis of the pnp–deaD genetic region reveals membrane lipoprotein NlpI as an independent participant in cold acclimatization of Salmonella enterica serovar Typhimurium

Rouf, S. F., Anwar, N., Clements, M. O. and Rhen, M.
BGI

.. Although S. Typhimurium pnp and nlpI are separated by 109 base pairs, the promoter prediction software bprom (www.Softberry.com) failed to define any tentative nlpI promoter within this intergenic region (data not shown). ...


Applied Microbiology and Biotechnology
Volume 90, Issue 2 , pp 625-634 DOI: 10.1007/s00253-011-3121-x

Co-transcription of the celC gene cluster in Clostridium thermocellum

Michael Newcomb, Jonathan Millen, Chun-Yu Chen, J. H. David Wu
1. Department of Chemical Engineering, University of Rochester, Room 206 Gavett Hall, Rochester, NY, 14627-0166, USA 2. Novozymes North America Inc., 77 Perry Chapel Church Road, Franklinton, NC, 27525, USA

... The palindromic GlyR3 binding site (Newcomb et al. 2007) is bolded. The ?10 and ?35 sigma factor binding sites predicted by BProm (http:// linux1.softberry.com/berry. phtml, accessed 3 January 2011) are noted by a solid and a dashed box, respectively 630 ...


BMC Microbiology
2011, 11:90 doi:10.1186/1471-2180-11-90

Integration Host Factor (IHF) binds to the promoter region of the phtD operon involved in phaseolotoxin synthesis in P. syringae pv. phaseolicola NPS3121

Arvizu-Gomez et al.,
1 Departamento de Ingenieria Genetica, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional Unidad Irapuato, Apdo Postal 629, CP 36821, Irapuato, Gto, Mexico 2 Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Apdo Postal 629, CP 36821, Irapuato, Gto, Mexico

...we evaluated the presence of putative cis-acting elements within the phtD promoter region using a transcription factor search program (BPROM, http://www.softberry.com webcite) [26]....


The Journal of Biological Chemistry
November 11, 2011 , 286, 38854-38864, doi: 10.1074/jbc.M111.260992

Identification of a Novel Streptococcal Adhesin P (SadP) Protein Recognizing Galactosyl-a1–4-galactose-containing Glycoconjugates

Kouki et al.,
‡Department of Medical Biochemistry and Genetics, University of Turku, Kiinamyllynkatu 10, Turku FI-20520, Finland, the ?Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, P.O.B. 56, Helsinki FI-00014, Finland,

... terminators. SadP was not located in an operon, and promoter sequences typical for Gram-positive bacteria upstream of the gene and a Rho-independent terminator were predicted using the program Bprom on the Softberry server. ...


BMC Microbiology
2011, 11:72 doi:10.1186/1471-2180-11-72

Contribution of SecDF to Staphylococcus aureus resistance and expression of virulence factors

Quiblier et al.,
1 Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland 2 Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistr. 100, 8091 Zurich, Switzerland

...Promoter predictions were performed by BPROM http://linux1.softberry.com/berry.phtml...


J. Bacteriol.
July 2011 vol. 193 no. 13 3207-3219 doi: 10.1128/JB.00044-11

The Anaerobe-Specific Orange Protein Complex of Desulfovibrio vulgaris Hildenborough Is Encoded by Two Divergent Operons Coregulated by ?54 and a Cognate Transcriptional Regulator

Fievet et al.,
1Laboratoire Interactions et Modulateurs de Reponses, Institut de Microbiologie de la Mediterranee, CNRS 13402 Marseille Cedex 20, France 2Laboratoire d'Ingenierie des Systemes Macromoleculaires, Institut de Microbiologie de la Mediterranee, CNRS 13402 Marseille Cedex 20, France

. lactate/sulfate conditions. To characterize the cis elements required for transcription of the orp1 and orp2 operons, in silico analyses were carried out using the Softberry (BProm) and PromScan algorithms. These analyses predicted ...


Appl. Environ. Microbiol.
May 2011 vol. 77 no. 9 2823-2830 doi: 10.1128/AEM.02633-10

Important Role of Class I Heat Shock Genes hrcA and dnaK in the Heat Shock Response and the Response to pH and NaCl Stress of Group I Clostridium botulinum Strain ATCC 3502

Selby et al.,
1Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland 2Center for Biomolecular S