List of gene prediction software

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

Name Description Species References
ATGpr Identifies translational initiation sites in cDNA sequences
AUGUSTUS Eukaryote gene predictor Eukaryotes [1]
BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program
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 [2]
FGENESH HMM-based gene structure prediction: multiple genes, both chains Eukaryotes
FRAMED Find genes and frameshift in G+C rich prokaryote sequences Prokaryotes [3]
GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data [4]
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
GENEPARSER Parse DNA sequences into introns and exons
GeneMark Family of self-training gene prediction programs Prokaryotes, Eukaryotes,

Metagenomes

 [5]
GeneTack Predicts genes with frameshifts in prokaryote genomes Prokaryotes [6]
GENOMESCAN Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms
GENSCAN Finds genes using Fourier transform [7]
GLIMMER Finds genes in microbial DNA Prokaryotes
GLIMMERHMM Eukaryotic gene-finding system Eukaryotes [8]
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 [9]
mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays Eukaryotes [10]
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

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. ↑ Keilwagen J, Wenk M, Erickson J L, Schattat M H, Grau J, Hartung F. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016; 44 (9): e89
  5. ↑ Lukashin A. and Borodovsky M. (1998). "GeneMark.hmm: new solutions for gene finding". Nucleic Acids Research. 26 (4): 1107–1115. PMC 147337 Freely accessible. PMID 9461475. doi:10.1093/nar/26.4.1107.
  6. ↑ 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. PMID 20556861. doi:10.1142/S0219720010004847.
  7. ↑ Burge C, Karlin S (1997). "Prediction of complete gene structures in human genomic DNA". J. Mol. Biol. 268 (1): 78–94. PMID 9149143. doi:10.1006/jmbi.1997.0951.
  8. ↑ Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879
  9. ↑ 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.
  10. ↑ Gan, X, Stegle, O., Behr, J, et al., Rätsch, G., Mott, R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana, Nature 477, 419–423.
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