List of gene prediction software

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

Name DescriptionSpeciesReferences
FragGeneScan Predicting genes in complete genomes and sequencing ReadsProkaryotes, Metagenomes [1]
ATGpr Identifies translational initiation sites in cDNA sequences[2]
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) [3]
AUGUSTUS Eukaryote gene predictorEukaryotes[4]
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[5]
FGENESH HMM-based gene structure prediction: multiple genes, both chainsEukaryotes[6]
FRAMED Find genes and frameshift in G+C rich prokaryote sequencesProkaryotes[7]
GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data [8][9]
GENIUS Links ORFs in complete genomes to protein 3D structures
geneid Program to predict genes, exons, splice sites, and other signals along DNA sequencesEukaryotes[10]
GENEPARSER Parse DNA sequences into introns and exons
GeneMark Family of self-training gene prediction programsProkaryotes, Eukaryotes,

Metagenomes

 [11][12][13][14]
GeneTack Predicts genes with frameshifts in prokaryote genomesProkaryotes[15]
GENOMESCAN Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms
GENSCAN Finds genes using Fourier transform[16]
GLIMMER Finds genes in microbial DNAProkaryotes
GLIMMERHMM Eukaryotic gene-finding systemEukaryotes[17]
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[18]
mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arraysEukaryotes[19]
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
This list is incomplete; you can help by adding missing items with reliable sources.

See also

References
  1. Rho M, Tang H, Ye Y (November 2010). "FragGeneScan: predicting genes in short and error-prone reads". Nucleic Acids Research. 38 (20): e191. doi:10.1093/nar/gkq747. PMC 2978382. PMID 20805240.
  2. "Prediction of Translation Initiation ATG". atgpr.dbcls.jp. Retrieved 2018-09-08.
  3. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (March 2010). "Prodigal: prokaryotic gene recognition and translation initiation site identification". BMC Bioinformatics. 11: 119. doi:10.1186/1471-2105-11-119. PMC 2848648. PMID 20211023.
  4. Keller O, Kollmar M, Stanke M, Waack S (March 2011). "A novel hybrid gene prediction method employing protein multiple sequence alignments". Bioinformatics (Oxford, England). 27 (6): 757–63. doi:10.1093/bioinformatics/btr010. PMID 21216780.
  5. Foissac S, Gouzy J, Rombauts S, Mathé C, Amselem J, Sterck L, de Peer YV, Rouzé P, Schiex T (May 2008). "Genome annotation in plants and fungi: EuGene as a model platform". Current Bioinformatics. 3 (2): 87–97. doi:10.2174/157489308784340702.
  6. Salamov AA, Solovyev VV (April 2000). "Ab initio gene finding in Drosophila genomic DNA". Genome Research. 10 (4): 516–22. doi:10.1101/gr.10.4.516. PMC 310882. PMID 10779491.
  7. Schiex T, Gouzy J, Moisan A, de Oliveira Y (July 2003). "FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences". Nucleic Acids Research. 31 (13): 3738–41. doi:10.1093/nar/gkg610. PMC 169016. PMID 12824407.
  8. Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F (May 2016). "Using intron position conservation for homology-based gene prediction". Nucleic Acids Research. 44 (9): e89. doi:10.1186/s12859-018-2203-5. PMC 4872089. PMID 26893356.
  9. Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J (May 2018). "Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi". BMC Bioinformatics. 19 (1): 189. doi:10.1093/nar/gkw092. PMC 5975413. PMID 29843602.
  10. Blanco, Enrique; Parra, Genís; Guigó, Roderic (June 2007), "Using geneid to Identify Genes", Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Chapter 4: 4.3.1–4.3.28, doi:10.1002/0471250953.bi0403s18, ISBN 978-0471250951, PMID 18428791
  11. Lukashin AV, Borodovsky M (February 1998). "GeneMark.hmm: new solutions for gene finding". Nucleic Acids Research. 26 (4): 1107–15. doi:10.1093/nar/26.4.1107. PMC 147337. PMID 9461475.
  12. Besemer J, Lomsadze A, Borodovsky M (June 2001). "GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions". Nucleic Acids Research. 29 (12): 2607–18. doi:10.1093/nar/29.12.2607. PMC 55746. PMID 11410670.
  13. Lomsadze A, Burns PD, Borodovsky M (September 2014). "Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm". Nucleic Acids Research. 42 (15): e119. doi:10.1093/nar/gku557. PMC 4150757. PMID 24990371.
  14. Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542. PMID 20403810.
  15. Antonov I, Borodovsky M (June 2010). "Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm". Journal of Bioinformatics and Computational Biology. 8 (3): 535–51. doi:10.1142/S0219720010004847. PMID 20556861.
  16. Burge C, Karlin S (April 1997). "Prediction of complete gene structures in human genomic DNA". Journal of Molecular Biology. 268 (1): 78–94. CiteSeerX 10.1.1.115.3107. doi:10.1006/jmbi.1997.0951. PMID 9149143.
  17. Majoros WH, Pertea M, Salzberg SL (November 2004). "TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders". Bioinformatics. 20 (16): 2878–9. doi:10.1093/bioinformatics/bth315. PMID 15145805.
  18. Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, et al. (November 2009). "mGene: accurate SVM-based gene finding with an application to nematode genomes". Genome Research. 19 (11): 2133–43. doi:10.1101/gr.090597.108. PMC 2775605. PMID 19564452.
  19. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, et al. (August 2011). "Multiple reference genomes and transcriptomes for Arabidopsis thaliana". Nature. 477 (7365): 419–23. Bibcode:2011Natur.477..419G. doi:10.1038/nature10414. PMC 4856438. PMID 21874022.
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