List of gene prediction software

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This list of gene prediction software is a compilation of software tools and web portals used for gene prediction.

Ab initio approaches

Name	Description	Species	Links	References
ATGpr	identifying translational initiation sites in cDNA sequences
AUGUSTUS	Eukaryote gene predictor	Eukaryotes	Predict Train AUGUSTUS	[1]
BGF	hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program		webserver
DIOGENES	a system for fast detection of coding regions in short genomic sequences
Dragon Promoter Finder	software for recognition of vertebrate RNA Polymerase II promoters
EUGENE	Integrative gene finding	Eukaryotes and prokaryotes	EuGene webserver	[2]
FGENESH	HMM-based gene structure prediction (multiple genes, both chains)	Eukaryotes	webserver
FRAMED	find genes and frameshift in G+C rich prokaryotic sequences	Prokaryotes	webserver	[3]
GENIUS	linking ORFs in complete genomes to protein 3D structures
geneid	program to predict genes, exons, splice sites and other signals along a DNA sequence	Eukaryotes	webserver
GENEPARSER	Parse a DNA sequence into introns and exons
GeneMark	family of gene prediction programs	Prokaryotes+Eukaryotes	webserver	[4]
GeneTack	prediction of genes with frameshifts in prokaryotic genomes	Prokaryotes	webserver	[5]
GENOMESCAN	predicts locations and exon-intron structures of genes in genomic sequences from a variety of organisms.		webserver
GENSCAN	finding genes using Fourier transform		webserver	[6]
GLIMMER	finding genes in microbial DNA	Prokaryotes	sourcecode webserver
GLIMMERHMM	Eukaryotic gene-finding System	Eukaryotes	webserver	[7]
GrailEXP	predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence
mGene	a Support-Vector Machine based system for finding genes	Eukaryotes	webserver	[8]
mGene.ngs	a SVM based system for finding genes using heterogeneous information (RNA-seq, tiling arrays)	Eukaryotes		[9]
MORGAN	a decision tree system for finding genes in vertebrate DNA	Eukaryotes
NIX	web tool for combining results from different programs (GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN)
NNPP	promoter prediction by neural network
NNSPLICE	splice site prediction by neural network
ORF FINDER	a graphical analysis tool which finds all open reading frames
Regulatory Sequence Analysis Tools	provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.
SPLICEPREDICTOR	a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models	Eukaryotes
VEIL	hidden markov model for finding genes in vertebrate DNA Server	Eukaryotes

See also

• Gene prediction
• List of RNA structure prediction software
• List of software for molecular mechanics modeling

References

1. Keller O, Kollmar M, Stanke M, Waack S. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics. 2011 Mar 15;27(6):757-63.
2. Foissac, S., Gouzy, J.P., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van de Peer, Y., Rouzé, P., Schiex, T. (2008) Genome Annotation in Plants and Fungi: EuGene as a model platform. Curr. Bioinform. 3, 87-97
3. Schiex T, Gouzy J, Moisan A, de Oliveira Y. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3738-41
4. Lukashin A. and Borodovsky M. (1998). "GeneMark.hmm: new solutions for gene finding". Nucleic Acids Research 26 (4): 1107–1115. doi:10.1093/nar/26.4.1107. PMC 147337. PMID 9461475.
5. Antonov I. and Borodovsky M. (2010). "Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm". J Bioinform Comput Biol. 8 (3): 535–51. doi:10.1142/S0219720010004847. PMID 20556861.
6. Burge C, Karlin S (1997). "Prediction of complete gene structures in human genomic DNA". J. Mol. Biol. 268 (1): 78–94. doi:10.1006/jmbi.1997.0951. PMID 9149143.
7. Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879
8. Schweikert, G., Zien, A., et al., Rätsch, G., mGene: Accurate SVM-based gene finding with an application to nematode genomes, Genome Res. Nov 2009; 19(11): 2133–2143.
9. Gan, X, Stegle, O., Behr, J, et al., Rätsch, G., Mott, R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana, Nature 477, 419–423.