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The programs usage in Scientific publications

FGENESH is very fast and accurate ab initio gene prediction program - 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.

Our best gene finder Eukaryotic genome annotation pipeline Fgenesh++ (see flowchart) cannot be accessed at our site due to computing resources limitations but can be licensed for automatic annotation of genomes with quality similar to that of manual annotation. Fgenesh++ includes the following steps:

• a) Mapping known mRNAs from RefSeq or full-length transcripts assembled from NGS RNASeq reads by Trinity (MRNA_MAP program);
• b) Mapping known proteins (from a subset of OrthoDB or NR database) to a genome (PROT_MAP program);
• c) Identification of splice sites by mapping a set of known ESTs or partial transcripts assembled from NGS RNASeq reads;
• d) Identification of ab initio gene models.

To find genes in Bacterial sequences click here.

FGENES, FGENES-M, FGENESH_GC and SPLM can be used on human sequences only.
BESTORF and Fsplice can be used with 296 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]