List of gene prediction software

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

Name DescriptionSpeciesReferences
ATGpr Identifies translational initiation sites in cDNA sequences[1]
PRODIGAL Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models. Prokaryotes, Metagenomes (metaProdigal) [2]
AUGUSTUS Eukaryote gene predictorEukaryotes[3]
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 findingEukaryotes, prokaryotes[4]
FGENESH HMM-based gene structure prediction: multiple genes, both chainsEukaryotes[5]
FRAMED Find genes and frameshift in G+C rich prokaryote sequencesProkaryotes[6]
GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data [7][8]
GENIUS Links ORFs in complete genomes to protein 3D structures
geneid Program to predict genes, exons, splice sites, and other signals along DNA sequencesEukaryotes[9]
GENEPARSER Parse DNA sequences into introns and exons
GeneMark Family of self-training gene prediction programsProkaryotes, Eukaryotes,

Metagenomes

 [10][11][12][13]
GeneTack Predicts genes with frameshifts in prokaryote genomesProkaryotes[14]
GENOMESCAN Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms
GENSCAN Finds genes using Fourier transform[15]
GLIMMER Finds genes in microbial DNAProkaryotes
GLIMMERHMM Eukaryotic gene-finding systemEukaryotes[16]
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 genesEukaryotes[17]
mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arraysEukaryotes[18]
MORGAN Decision tree system to find genes in vertebrate DNAEukaryotes
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 modelsEukaryotes
VEIL Hidden Markov model to find genes in vertebrate DNA ServerEukaryotes

See also

References

  1. ↑ "Prediction of Translation Initiation ATG". atgpr.dbcls.jp. Retrieved 2018-09-08.
  2. ↑ Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.; Land, Miriam L.; Larimer, Frank W.; Hauser, Loren J. (2010-03-08). "Prodigal: prokaryotic gene recognition and translation initiation site identification". BMC Bioinformatics. 11: 119. doi:10.1186/1471-2105-11-119. ISSN 1471-2105.
  3. ↑ 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.
  4. ↑ 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
  5. ↑ Salamov, Asaf A., and Victor V. Solovyev. "Ab initio gene finding in Drosophila genomic DNA." Genome research 10.4 (2000): 516-522.
  6. ↑ 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
  7. ↑ Keilwagen J, Wenk M, Erickson J L, Schattat M H, Grau J, Hartung F (2016). "Using intron position conservation for homology-based gene prediction". Nucleic Acids Res. 44 (9). PMID 26893356.
  8. ↑ Keilwagen J, Hartung F, Paulini M, Twardziok S O, Grau J (2018). "Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi". BMC Bioinformatics. 19: 189. PMID 29843602.
  9. ↑ Blanco, Enrique; Parra, Genís; Guigó, Roderic (June 2007), "Using geneid to Identify Genes", Current Protocols in Bioinformatics, John Wiley & Sons, Inc., pp. 4.3.1–4.3.28, doi:10.1002/0471250953.bi0403s18, ISBN 0471250953, retrieved 2018-09-17
  10. ↑ 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.
  11. ↑ Besemer J, Lomsadze A, Borodovsky M (2001). "GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions". Nucleic Acids Res. 29 (12): 2607–18. doi:10.1093/nar/29.12.2607. PMC 55746. PMID 11410670.
  12. ↑ Lomsadze A, Burns PD, Borodovsky M (2014). "Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm". Nucleic Acids Res. 42 (15): e119. doi:10.1093/nar/gku557. PMC 4150757. PMID 24990371.
  13. ↑ Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Res. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542. PMID 20403810.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ Majoros W.H., Pertea M., Salzberg S.L. "TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders". Bioinformatics. 20: 2878–2879. doi:10.1093/bioinformatics/bth315.
  17. ↑ Schweikert G., Zien A., Rätsch G. (2009). "mGene: Accurate SVM-based gene finding with an application to nematode genomes". Genome Res. 19 (11): 2133–2143. doi:10.1101/gr.090597.108. PMC 2775605.
  18. ↑ Gan X, Stegle O., Behr J; et al. "Rätsch, G., Mott, R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana". Nature. 477: 419–423. doi:10.1038/nature10414.
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