This list of gene prediction software is a compilation of software tools and web portals used for gene prediction.
Ab initio approaches
|
| ATGpr | identifying 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 | a system for fast detection of coding regions in short genomic sequences | | | |
| Dragon Promoter Finder | software for recognition of vertebrate RNA Polymerase II promoters | | | |
| EUGENE | gene finding for Arabidopsis thaliana | Arabidopsis thaliana | | |
| FGENESH | HMM-based gene structure prediction (multiple genes, both chains) | Eukaryotes | webserver | |
| FRAMED | find genes and frameshift in G+C rich prokaryotic sequences | Prokaryotes | webserver | [2] |
| GENIUS | linking ORFs in complete genomes to protein 3D structures | | | |
| geneid | program to predict genes, exons, splice sites and other signals along a DNA sequence | Eukaryotes | webserver | |
| GENEPARSER | Parse a DNA sequence into introns and exons | | | |
| GeneMark | family of gene prediction programs | Prokaryotes+Eukaryotes | webserver | |
| GeneMark.hmm | gene prediction program for prokaryotes and eukaryotes | Prokaryotes+Eukaryotes | webserver | [3] |
| GeneTack | prediction of genes with frameshifts in prokaryotic genomes | Prokaryotes | webserver | [4] |
| GENOMESCAN | predicts locations and exon-intron structures of genes in genomic sequences from a variety of organisms. | | webserver | |
| GENSCAN | finding genes using Fourier transform | | webserver | [5] |
| GLIMMER | finding genes in microbial DNA | Prokaryotes | sourcecode webserver | |
| GLIMMERHMM | Eukaryotic gene-finding System | Eukaryotes | webserver | [6] |
| GrailEXP | predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence | | | |
| MORGAN | a decision tree system for finding genes in vertebrate DNA | Eukaryotes | | |
| NIX | web tool for combining results from different programs (GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN) | | | |
| NNPP | promoter prediction by neural network | | | |
| NNSPLICE | splice site prediction by neural network | | | |
| ORF FINDER | a graphical analysis tool which finds all open reading frames | | | |
| Regulatory Sequence Analysis Tools | provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. | | | |
| SPLICEPREDICTOR | a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models | Eukaryotes | | |
| VEIL | hidden markov model for finding genes in vertebrate DNA Server | Eukaryotes | | |
See also
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.
- ^ 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". NAR 26 (4): 1107–1115. doi:10.1093/nar/26.4.1107. PMC 147337. PMID 9461475. //www.ncbi.nlm.nih.gov/pmc/articles/P MC147337/.
- ^ 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
