List of gene prediction software
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This is a list of software tools and web portals used for gene prediction.
Ab initio methods
| Name | Description | Species | Links | References |
|---|---|---|---|---|
| ATGpr | Identifies translational initiation sites in cDNA sequences | |||
| AUGUSTUS | Eukaryote gene predictor | Eukaryotes | Predict Train AUGUSTUS | [1] |
| BGF | Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program | webserver | ||
| 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 | EuGene webserver | [2] |
| FGENESH | HMM-based gene structure prediction: multiple genes, both chains | Eukaryotes | webserver | |
| FRAMED | Find genes and frameshift in G+C rich prokaryote sequences | Prokaryotes | webserver | [3] |
| 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 | webserver | |
| GENEPARSER | Parse DNA sequences into introns and exons | |||
| GeneMark | Family of gene predicting programs | Prokaryotes+Eukaryotes | webserver | [4] |
| GeneTack | Predicts genes with frameshifts in prokaryote genomes | Prokaryotes | webserver | [5] |
| GENOMESCAN | Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms | webserver | ||
| GENSCAN | Finds genes using Fourier transform | webserver | [6] | |
| GLIMMER | Finds genes in microbial DNA | Prokaryotes | sourcecode webserver | |
| GLIMMERHMM | Eukaryotic gene-finding system | Eukaryotes | webserver | [7] |
| 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 | webserver | [8] |
| mGene.ngs | SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays | Eukaryotes | [9] | |
| 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
- Gene prediction
- List of RNA structure prediction software
- Comparison of software for molecular mechanics modeling
References
- ↑ 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
- ↑ 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
- ↑ 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. - ↑ 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. doi:10.1006/jmbi.1997.0951. PMID 9149143.
- ↑ Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879
- ↑ 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.
- ↑ 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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