FGENESH

FGENESH HMM based Gene structure prediction
FGENES Pattern based Human Gene structure
FGENES-M Multiple variants of Gene structure
FGENESH-M Prediction of multiple variants potential genes in genomic DNA
FGENESH_GC (with possible donor GC) HMM based Human Gene structure prediction
BESTORF Finding coding fragment EST/mRNA
FEX Finding potential 5'-, internal and 3'-coding exons
SPL Search for potential splice sites
SPLM Search for non-standard splice sites using weight matrices
RNASPL Search for exon-exon junction positions in cDNA
FSPLICE Find splice sites in genomic DNA

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).

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Select organism specific gene-finding parameters :
Total 353 genome-specific parameters are available for genefinders of FGENESH suite

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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