Software:List of gene prediction software
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Short description: Wikipedia list article
This is a list of software tools and web portals used for gene prediction.
Name | Description | Species | References |
---|---|---|---|
FINDER | Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences | Eukaryotes | [1] |
FragGeneScan | Predicting genes in complete genomes and sequencing Reads | Prokaryotes, Metagenomes | [2] |
ATGpr | Identifies translational initiation sites in cDNA sequences | [3] | |
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) | [4] |
AUGUSTUS | Eukaryote gene predictor | Eukaryotes | [5] |
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 | [6] |
FGENESH | HMM-based gene structure prediction: multiple genes, both chains | Eukaryotes | [7] |
FRAMED | Find genes and frameshift in G+C rich prokaryote sequences | Prokaryotes | [8] |
GeMoMa | Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data | [9][10] | |
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 | [11] |
GENEPARSER | Parse DNA sequences into introns and exons | ||
GeneMark | Family of self-training gene prediction programs | Prokaryotes, Eukaryotes,
Metagenomes |
[12][13][14][15] |
GeneTack | Predicts genes with frameshifts in prokaryote genomes | Prokaryotes | [16] |
GENOMESCAN | Predicts locations and exon-intron structures of genes in genome sequences from a variety of organisms | ||
GENSCAN | Finds genes using Fourier transform | [17] | |
GLIMMER | Finds genes in microbial DNA | Prokaryotes | |
GLIMMERHMM | Eukaryotic gene-finding system | Eukaryotes | [18] |
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 | [19] |
mGene.ngs | SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays | Eukaryotes | [20] |
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 | ||
PHANOTATE | A tool to annotate phage genomes. | Phages | [21] |
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
- ↑ "FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences". BMC Bioinformatics 44 (9): e89. Apr 2021. doi:10.1186/s12859-021-04120-9. PMID 33879057.
- ↑ "FragGeneScan: predicting genes in short and error-prone reads". Nucleic Acids Research 38 (20): e191. November 2010. doi:10.1093/nar/gkq747. PMID 20805240.
- ↑ "Prediction of Translation Initiation ATG". http://atgpr.dbcls.jp.
- ↑ "Prodigal: prokaryotic gene recognition and translation initiation site identification". BMC Bioinformatics 11: 119. March 2010. doi:10.1186/1471-2105-11-119. PMID 20211023.
- ↑ "A novel hybrid gene prediction method employing protein multiple sequence alignments". Bioinformatics 27 (6): 757–63. March 2011. doi:10.1093/bioinformatics/btr010. PMID 21216780.
- ↑ "Genome annotation in plants and fungi: EuGene as a model platform.". Current Bioinformatics 3 (2): 87–97. May 2008. doi:10.2174/157489308784340702. https://www.ingentaconnect.com/content/ben/cbio/2008/00000003/00000002/art00003.
- ↑ "Ab initio gene finding in Drosophila genomic DNA". Genome Research 10 (4): 516–22. April 2000. doi:10.1101/gr.10.4.516. PMID 10779491.
- ↑ "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. July 2003. doi:10.1093/nar/gkg610. PMID 12824407.
- ↑ "Using intron position conservation for homology-based gene prediction". Nucleic Acids Research 44 (9): e89. May 2016. doi:10.1186/s12859-018-2203-5. PMID 26893356.
- ↑ "Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi". BMC Bioinformatics 19 (1): 189. May 2018. doi:10.1093/nar/gkw092. PMID 29843602.
- ↑ Blanco, Enrique; Parra, Genís; Guigó, Roderic (June 2007), "Using geneid to Identify Genes" (in en), 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
- ↑ "GeneMark.hmm: new solutions for gene finding". Nucleic Acids Research 26 (4): 1107–15. February 1998. doi:10.1093/nar/26.4.1107. PMID 9461475.
- ↑ "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. June 2001. doi:10.1093/nar/29.12.2607. PMID 11410670.
- ↑ "Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm". Nucleic Acids Research 42 (15): e119. September 2014. doi:10.1093/nar/gku557. PMID 24990371.
- ↑ "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research 38 (12): e132. July 2010. doi:10.1093/nar/gkq275. PMID 20403810.
- ↑ "Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm". Journal of Bioinformatics and Computational Biology 8 (3): 535–51. June 2010. doi:10.1142/S0219720010004847. PMID 20556861.
- ↑ "Prediction of complete gene structures in human genomic DNA". Journal of Molecular Biology 268 (1): 78–94. April 1997. doi:10.1006/jmbi.1997.0951. PMID 9149143.
- ↑ "TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders". Bioinformatics 20 (16): 2878–9. November 2004. doi:10.1093/bioinformatics/bth315. PMID 15145805.
- ↑ "mGene: accurate SVM-based gene finding with an application to nematode genomes". Genome Research 19 (11): 2133–43. November 2009. doi:10.1101/gr.090597.108. PMID 19564452.
- ↑ "Multiple reference genomes and transcriptomes for Arabidopsis thaliana". Nature 477 (7365): 419–23. August 2011. doi:10.1038/nature10414. PMID 21874022. Bibcode: 2011Natur.477..419G.
- ↑ McNair, Katelyn; Zhou, Carol; Dinsdale, Elizabeth A.; Souza, Brian; Edwards, Robert A. (2019-11-01). "PHANOTATE: a novel approach to gene identification in phage genomes" (in en). Bioinformatics 35 (22): 4537–4542. doi:10.1093/bioinformatics/btz265. ISSN 1367-4803. https://academic.oup.com/bioinformatics/article/35/22/4537/5480131.