List of gene prediction software
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 | [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 predictor | Eukaryotes | [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 finding | Eukaryotes | [4] |
FGENESH | HMM-based gene structure prediction: multiple genes, both chains | Eukaryotes | [5] |
FRAMED | Find genes and frameshift in G+C rich prokaryote sequences | Prokaryotes | [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 sequences | Eukaryotes | [9] |
GENEPARSER | Parse DNA sequences into introns and exons | ||
GeneMark | Family of self-training gene prediction programs | Prokaryotes, Eukaryotes,
Metagenomes |
[10][11][12][13] |
GeneTack | Predicts genes with frameshifts in prokaryote genomes | Prokaryotes | [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 DNA | Prokaryotes | |
GLIMMERHMM | Eukaryotic gene-finding system | Eukaryotes | [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 genes | Eukaryotes | [17] |
mGene.ngs | SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays | Eukaryotes | [18] |
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
- "Prediction of Translation Initiation ATG". atgpr.dbcls.jp. Retrieved 2018-09-08.
- 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. PMC 2848648.
- 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.
- 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
- Salamov, Asaf A., and Victor V. Solovyev. "Ab initio gene finding in Drosophila genomic DNA." Genome research 10.4 (2000): 516-522.
- 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
- 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): e89. doi:10.1186/s12859-018-2203-5. PMC 4872089. PMID 26893356.CS1 maint: multiple names: authors list (link)
- 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 (9): 189. doi:10.1093/nar/gkw092. PMC 5975413. PMID 29843602.CS1 maint: multiple names: authors list (link)
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- Burge C, Karlin S (1997). "Prediction of complete gene structures in human genomic DNA". J. Mol. Biol. 268 (1): 78–94. CiteSeerX 10.1.1.115.3107. doi:10.1006/jmbi.1997.0951. PMID 9149143.
- Majoros W.H., Pertea M., Salzberg S.L. (2004). "TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders". Bioinformatics. 20 (16): 2878–2879. doi:10.1093/bioinformatics/bth315. PMID 15145805.CS1 maint: multiple names: authors list (link)
- 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. PMID 19564452.CS1 maint: multiple names: authors list (link)
- Gan X, Stegle O, Behr J, et al. (2011). "Rätsch, G., Mott, R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana". Nature. 477 (7365): 419–423. doi:10.1038/nature10414. PMC 4856438. PMID 21874022.
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