List of gene prediction software

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

Ab initio methods

Name	Description	Species	Links	References
ATGpr	Identifies 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	Fast detection of coding regions in short genome sequences
Dragon Promoter Finder	Program to recognize vertebrate RNA polymerase II promoters
EUGENE	Integrative gene finding	Eukaryotes, 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 prokaryote sequences	Prokaryotes	webserver	[3]
GENIUS	Links ORFs in complete genomes to protein 3D structures
geneid	Program to predict genes, exons, splice sites, and other signals along DNA sequences	Eukaryotes	webserver
GENEPARSER	Parse DNA sequences into introns and exons
GeneMark	Family of gene predicting programs	Prokaryotes+Eukaryotes	webserver	[4]
GeneTack	Predicts genes with frameshifts in prokaryote genomes	Prokaryotes	webserver	[5]
GENOMESCAN	Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms		webserver
GENSCAN	Finds genes using Fourier transform		webserver	[6]
GLIMMER	Finds 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 repeat elements in DNA sequence
mGene	Support-vector machine (SVM) based system to find genes	Eukaryotes	webserver	[8]
mGene.ngs	SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays	Eukaryotes		[9]
MORGAN	Decision tree system to find genes in vertebrate DNA	Eukaryotes
NIX	Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN
NNPP	Neural network promoter prediction
NNSPLICE	Neural network splice site prediction
ORF FINDER	Graphical analysis tool to find all open reading frames
Regulatory Sequence Analysis Tools	Series of modular computer programs to detect regulatory signals in non-coding sequences
SPLICEPREDICTOR	Method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models	Eukaryotes
VEIL	Hidden Markov model to find genes in vertebrate DNA Server	Eukaryotes

See also

• Gene prediction
• List of RNA structure prediction software
• Comparison 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.