List of gene prediction software
This is a list of software tools and web portals used for gene prediction.
Name | Description | Species | References |
---|---|---|---|
FragGeneScan | Predicting genes in complete genomes and sequencing Reads | Prokaryotes, 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 predictor | Eukaryotes | [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 finding | Eukaryotes | [5] |
FGENESH | HMM-based gene structure prediction: multiple genes, both chains | Eukaryotes | [6] |
FRAMED | Find genes and frameshift in G+C rich prokaryote sequences | Prokaryotes | [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 sequences | Eukaryotes | [10] |
GENEPARSER | Parse DNA sequences into introns and exons | ||
GeneMark | Family of self-training gene prediction programs | Prokaryotes, Eukaryotes,
Metagenomes |
[11][12][13][14] |
GeneTack | Predicts genes with frameshifts in prokaryote genomes | Prokaryotes | [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 DNA | Prokaryotes | |
GLIMMERHMM | Eukaryotic gene-finding system | Eukaryotes | [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 genes | Eukaryotes | [18] |
mGene.ngs | SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays | Eukaryotes | [19] |
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
- 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.
- "Prediction of Translation Initiation ATG". atgpr.dbcls.jp. Retrieved 2018-09-08.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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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