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



Gene Finding: Gene models construction, splice sites, protein-coding exons

The programs usage in Scientific publications

FGENESH is the fastest and most accurate ab initio gene prediction program available - for more details, see FGENESH help. Its variants that use similarity information: FGENESH+ (similar protein), FGENESH_C (similar cDNA), FEGENESH-2 (two homologous genomic sequences) greatly improve accuracy of gene prediction when such similarity information is available. These programs can be accessed here.

To find genes in Bacterial sequences click here.

Our two best gene finders cannot be accessed at our site due to computing resources limitations. These two are FGENESH++ (automated version of FGENESH+) and FGENESH++C, which maps known mRNA/EST sequences from RefSeq and then performs FGENESH++-like gene prediction, resulting in fully automatic annotation of quality similar to that of manual annotation.

FGENES, FGENES-M, FGENESH_GC and SPLM can be used on human sequences only.
BESTORF and Fsplice can be used with 353 organisms sequences.
SPL can be used for human, Drosophila, nematode, S.cerevisiae, and dicots.

FGENESH - HMM-based gene structure prediction (multiple genes, both chains) [Help] [Example]

FGENES - Pattern based human gene structure prediction (multiple genes, both chains) [Help] [Example]

FGENES-M - Pattern-based human multiple variants of gene structure prediction) [Help] [Example]

FGENESH-M - Prediction of multiple variants potential genes in genomic DNA [Example]

FGENESH_GC - HMM-based human gene prediction that allows donor splice site GC donor splice site structure [Help] [Example]

BESTORF - Finding potential coding fragment EST/mRNA [Help] [Example]

FEX - Finding potential 5'-, internal and 3'-coding exons [Help] [Example]

SPL - Search for potential splice sites [Help] [Example]

SPLM - Search for human potential splice sites using weight matrices [Help] [Example]

RNASPL - Search for exon-exon junction positions in cDNA [Help] [Example]

FSPLICE - find splice sites in genomic DNA [Example]


You can now view all human genes - both known and predicted by our newest FGENESH++C gene finder, - and also more than 20,000 human promoters predicted by our TSSW , in Softberry GenomeSequence Explorer. October, 2000 release of human genome draft is shown with known and predicted genes, while December, 2000 release is shown with both genes and promoters.

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