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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Promoter
Protein location
RNA structure
Protein structure
3d-explorer
SeqMan
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs

 

 

FGENESH

Reference: Solovyev V, Kosarev P, Seledsov I, Vorobyev D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006,7, Suppl 1: P. 10.1-10.12.

HMM-based gene structure prediction (multiple genes, both chains). The Fgenesh gene-finder was selected as the most accurate program for plant gene identification. Plant Molecular Biology (2005), 57, 3, 445-460: "Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions" (FGENESH identified 11% more correct gene models than GeneMark on a set of 1353 test genes).

Paste nucleotide sequence here:

Alternatively, load a local file with sequence in Fasta format:

Local file name:

Select organism specific gene-finding parameters :

Total 353 genome-specific parameters are available for genefinders of FGENESH suite

Advanced options [see example of value in (..)]:

get sequence from this position, i.e., consider the sequence starting from this position.
get sequence to this position, i.e., consider the sequence to and through this position.
Use condensed sequence.
print mRNA sequences for predicted genes.
print exons sequences for predicted genes.
if the weight of exon is less than the weight specified by this option, it is rejected from prediction process.
if a “bad” promoter is found while predicting, two variants of prediction are compared: the prediction made with the promoter in question and without it. Of these variants of prediction, the prediction displaying a better weight is chosen.
If a “bad” terminator is found during prediction process, two variants of prediction are compared: the variant when the terminator is taken into account and the variant without the terminator. Of all the possible variants of prediction, the variant with the best weight is chosen.
Set minimal first exon this length.
Set minimal internal exon this length.
Set minimal terminal exon this length.
Set minimal single exon this length.
Use translation table (1 - Standard (Default); 2 - Vertebrate Mitochondrial; 3 - Yeast Mitochondrial; 4 - Mold Mitochondrial, Protozoan Mitochondrial, Colenterate Mitochondrial, Mycoplasma, and Spiroplasma; 5 - Invertebrate Mitochondrial; 6 - Ciliate Nuclear, Dasycladacean Nuclear, and Hexamita Nuclear; 9 - Echinoderm Nuclear; 10 - Euplotid Nuclear; 11 - Bacterial; 12 - Alternative Yeast Nuclear; 13 - Ascidian Mitochondrial; 14 - Flatworm Mitochondrial; 15 - Blepharisma Macronuclear).
Put here other options, if any.

[Help] [Hide advanced options
[Example: Homo sapiens genomic beta globin region (HBB@) on chromosome 11]
[Example: Search in -chain]

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Most gene finding parameters presented here were trained by Softberry for its own use and distribution, using proprietary and publicly available data. Some of the parameters were created for our academic customers, including Broad Institute/MIT, Washington University, University of Minnesota and The Institute for Genomic Research (TIGR).


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Last modification date: 12 Dec 2013

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