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List of gene prediction software

From Wikipedia, the free encyclopedia

This list isincomplete; you can help byadding missing items.(December 2011)

This is a list ofsoftware tools andweb portals used forgene prediction.

NameDescriptionSpeciesReferences
FINDERAutomated software package to annotate eukaryotic genes fromRNA-Seq data and associated protein sequencesEukaryotes[1]
FragGeneScanPredicting genes in complete genomes and sequencing ReadsProkaryotes, Metagenomes[2]
ATGprIdentifies translational initiation sites incDNA sequencesHuman[3]
ProdigalIts 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]
AUGUSTUSEukaryote gene predictorEukaryotes[5]
BGFHidden Markov model (HMM) anddynamic programming basedab initio gene prediction program[6]
DIOGENESFast detection of coding regions in short genome sequences
Dragon Promoter FinderProgram to recognize vertebrateRNA polymerase II promotersVertebrates[7]
EasyGeneThe gene finder is based on ahidden Markov model (HMM) that is automatically estimated for a new genome.Prokaryotes[8][9]
EuGeneIntegrative gene findingProkaryotes, Eukaryotes[10][11]
FGENESHHMM-based gene structure prediction: multiple genes, both chainsEukaryotes[12]
FrameDFind genes andframeshift inG+C richprokaryote sequencesProkaryotes, Eukaryotes[13]
GeMoMaHomology-based gene prediction based on amino acid and intron position conservation as well asRNA-Seq data[14][15]
GENIUS IILinksORFs in complete genomes to protein 3D structuresProkaryotes, Eukaryotes[16]
geneidProgram to predict genes, exons, splice sites, and other signals along DNA sequencesEukaryotes[17]
GeneParserParse DNA sequences into introns and exonsEukaryotes[18]
GeneMarkFamily of self-training gene prediction programsProkaryotes, Eukaryotes,

Metagenomes

[19][20][21][22]
GeneTackPredicts genes withframeshifts in prokaryote genomesProkaryotes[23]
GenomeScanPredicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms, GENSCAN server is the GenomeScan's predecessorVertebrate, Arabidopsis, Maize[24]
GENSCANPredicts the locations and exon-intron structures of genes in genome sequences from a variety of organismsVertebrate, Arabidopsis, Maize[25][26][27]
GLIMMERFinds genes in microbial DNAProkaryotes[28][29][30]
GLIMMERHMMEukaryotic gene-finding systemEukaryotes[31]
GrailEXPPredicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequenceHuman,Mus musculus,Arabidopsis thaliana,Drosophila melanogaster[32][33]
mGeneSupport-vector machine (SVM) based system to find genesEukaryotes[34]
mGene.ngsSVM based system to find genes using heterogeneous information: RNA-seq, tiling arraysEukaryotes[35]
MORGANDecision tree system to find genes in vertebrate DNAEukaryotes[36]
BioNIXWeb tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCANProkaryotes, Eukaryotes[37]
NNPPNeural network promoter predictionProkaryotes, Eukaryotes[38]
NNSPLICENeural network splice site predictionDrosophila, Human[39]
ORFfinderGraphical analysis tool to find allopen reading framesProkaryotes, Eukaryotes[40]
Regulatory Sequence Analysis ToolsSeries of modular computer programs to detect regulatory signals in non-coding sequencesFungi, Prokaryotes, Metazoa, Protist, Plants[41][42]
PHANOTATEA tool to annotatephage genomes.Phages[43]
SplicePredictorMethod to identify potential splice sites in (plant)pre-mRNA by sequence inspection using Bayesian statistical modelsEukaryotes[44]
VEILHidden Markov model to find genes in vertebrate DNA ServerEukaryotes[45]

See also

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References

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  1. ^Banerjee S, Bhandary P, Woodhouse M, Sen TZ, Wise RP, Andorf CM (Apr 2021)."FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences".BMC Bioinformatics.44 (9): e89.doi:10.1186/s12859-021-04120-9.PMC 8056616.PMID 33879057.
  2. ^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.
  3. ^Nishikawa, Tetsuo; Ota, Toshio; Isogai, Takao (2000-11-01)."Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences".Bioinformatics.16 (11):960–967.doi:10.1093/bioinformatics/16.11.960.ISSN 1367-4803.PMID 11159307.
  4. ^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.
  5. ^Keller O, Kollmar M, Stanke M, Waack S (March 2011)."A novel hybrid gene prediction method employing protein multiple sequence alignments".Bioinformatics.27 (6):757–63.doi:10.1093/bioinformatics/btr010.hdl:11858/00-001M-0000-0011-F244-D.PMID 21216780.
  6. ^Li, Heng; Liu, Jin-Song; Xu, Zhao; Jin, Jiao; Fang, Lin; Gao, Lei; Li, Yu-Dong; Xing, Zi-Xing; Gao, Shao-Gen; Liu, Tao; Li, Hai-Hong (2005-07-01)."Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome".Journal of Computer Science and Technology.20 (4):446–453.doi:10.1007/s11390-005-0446-x.ISSN 1860-4749.S2CID 13497894.
  7. ^Bajic, Vladimir B.; Seah, Seng Hong; Chong, Allen; Zhang, Guanglan; Koh, Judice L. Y.; Brusic, Vladimir (2002-01-01)."Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters".Bioinformatics.18 (1):198–199.doi:10.1093/bioinformatics/18.1.198.ISSN 1367-4803.PMID 11836231.
  8. ^Nielsen, P.; Krogh, A. (2005-12-15)."Large-scale prokaryotic gene prediction and comparison to genome annotation".Bioinformatics.21 (24):4322–4329.doi:10.1093/bioinformatics/bti701.ISSN 1367-4803.PMID 16249266.
  9. ^Larsen, Thomas Schou; Krogh, Anders (2003-06-03)."EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance".BMC Bioinformatics.4 (1): 21.doi:10.1186/1471-2105-4-21.ISSN 1471-2105.PMC 521197.PMID 12783628.
  10. ^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.
  11. ^Sallet, Erika; Gouzy, Jérôme; Schiex, Thomas (2019), Kollmar, Martin (ed.),"EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes",Gene Prediction: Methods and Protocols, Methods in Molecular Biology, vol. 1962, New York, NY: Springer, pp. 97–120,doi:10.1007/978-1-4939-9173-0_6,ISBN 978-1-4939-9173-0,PMID 31020556,S2CID 131776381, retrieved2021-11-24{{citation}}: CS1 maint: work parameter with ISBN (link)
  12. ^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.
  13. ^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.
  14. ^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.
  15. ^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.
  16. ^Yabuki, Yukimitsu; Mukai, Yuri; Swindells, Mark B.; Suwa, Makiko (2004-03-01)."GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures".Bioinformatics.20 (4):596–598.doi:10.1093/bioinformatics/btg478.ISSN 1367-4803.PMID 14751990.
  17. ^Blanco, Enrique; Parra, Genís; Guigó, Roderic (June 2007), "Using geneid to Identify Genes",Current Protocols in Bioinformatics, Chapter 4, John Wiley & Sons, Inc.: 4.3.1–4.3.28,doi:10.1002/0471250953.bi0403s18,ISBN 978-0471250951,PMID 18428791{{citation}}: CS1 maint: work parameter with ISBN (link)
  18. ^Snyder, Eric E.; Stormo, Gary D. (1995-04-21)."Identification of Protein Coding Regions In Genomic DNA".Journal of Molecular Biology.248 (1):1–18.doi:10.1006/jmbi.1995.0198.ISSN 0022-2836.PMID 7731036.
  19. ^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.
  20. ^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.
  21. ^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.
  22. ^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.
  23. ^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.
  24. ^Yeh, Ru-Fang; Lim, Lee P.; Burge, Christopher B. (2001-05-01)."Computational Inference of Homologous Gene Structures in the Human Genome".Genome Research.11 (5):803–816.doi:10.1101/gr.175701.ISSN 1088-9051.PMC 311055.PMID 11337476.
  25. ^Burge, Chris; Karlin, Samuel (1997-04-25)."Prediction of complete gene structures in human genomic DNA11Edited by F. E. Cohen".Journal of Molecular Biology.268 (1):78–94.doi:10.1006/jmbi.1997.0951.ISSN 0022-2836.PMID 9149143.
  26. ^Burge, Christopher B. (1998-01-01), Salzberg, Steven L.; Searls, David B.; Kasif, Simon (eds.),"Chapter 8 - Modeling dependencies in pre-mRNA splicing signals",New Comprehensive Biochemistry, Computational Methods in Molecular Biology, vol. 32, Elsevier, pp. 129–164,doi:10.1016/S0167-7306(08)60465-2,ISBN 978-0-444-82875-0, retrieved2021-11-24{{citation}}: CS1 maint: work parameter with ISBN (link)
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  28. ^Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C.; Salzberg, Steven L. (2007-01-19)."Identifying bacterial genes and endosymbiont DNA with Glimmer".Bioinformatics.23 (6):673–679.doi:10.1093/bioinformatics/btm009.ISSN 1460-2059.PMC 2387122.PMID 17237039.
  29. ^Delcher, A. (1999-12-01)."Improved microbial gene identification with GLIMMER".Nucleic Acids Research.27 (23):4636–4641.doi:10.1093/nar/27.23.4636.ISSN 1362-4962.PMC 148753.PMID 10556321.
  30. ^Salzberg, S. L.; Delcher, A. L.; Kasif, S.; White, O. (1998-01-01)."Microbial gene identification using interpolated Markov models".Nucleic Acids Research.26 (2):544–548.doi:10.1093/nar/26.2.544.ISSN 0305-1048.PMC 147303.PMID 9421513.
  31. ^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.
  32. ^Uberbacher, Edward C.; Hyatt, Doug; Shah, Manesh (2004)."GrailEXP and Genome Analysis Pipeline for Genome Annotation".Current Protocols in Bioinformatics.8 (1): 4.9.1–4.9.15.doi:10.1002/0471250953.bi0409s04.ISSN 1934-340X.PMID 18428726.
  33. ^Uberbacher, Edward C.; Hyatt, Doug; Shah, Manesh (2003)."GrailEXP and Genome Analysis Pipeline for Genome Annotation".Current Protocols in Human Genetics.39 (1): 6.5.1–6.5.15.doi:10.1002/0471142905.hg0605s39.ISSN 1934-8258.PMID 18428363.S2CID 21431978.
  34. ^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.
  35. ^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.
  36. ^"MORGAN".sites.stat.washington.edu. Retrieved2021-11-24.
  37. ^Bedő, Justin; Di Stefano, Leon; Papenfuss, Anthony T (November 2020)."Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix".GigaScience.9 (11).doi:10.1093/gigascience/giaa121.ISSN 2047-217X.PMC 7672450.PMID 33205815.
  38. ^Reese, Martin G (2001-12-01)."Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome".Computers & Chemistry.26 (1):51–56.doi:10.1016/S0097-8485(01)00099-7.ISSN 0097-8485.PMID 11765852.
  39. ^Reese, Martin G.; Eeckman, Frank H.; Kulp, David; Haussler, David (1997-01-01)."Improved Splice Site Detection in Genie".Journal of Computational Biology.4 (3):311–323.doi:10.1089/cmb.1997.4.311.PMID 9278062.
  40. ^"Home - ORFfinder - NCBI".www.ncbi.nlm.nih.gov. Retrieved2021-11-24.
  41. ^Santana-Garcia, Walter; Rocha-Acevedo, Maria; Ramirez-Navarro, Lucia; Mbouamboua, Yvon; Thieffry, Denis; Thomas-Chollier, Morgane; Contreras-Moreira, Bruno; van Helden, Jacques; Medina-Rivera, Alejandra (2019-01-01)."RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding".Computational and Structural Biotechnology Journal.17:1415–1428.doi:10.1016/j.csbj.2019.09.009.ISSN 2001-0370.PMC 6906655.PMID 31871587.
  42. ^Nguyen, Nga Thi Thuy; Contreras-Moreira, Bruno; Castro-Mondragon, Jaime A; Santana-Garcia, Walter; Ossio, Raul; Robles-Espinoza, Carla Daniela; Bahin, Mathieu; Collombet, Samuel; Vincens, Pierre; Thieffry, Denis; van Helden, Jacques (2018-05-02)."RSAT 2018: regulatory sequence analysis tools 20th anniversary".Nucleic Acids Research.46 (W1):W209–W214.doi:10.1093/nar/gky317.ISSN 0305-1048.PMC 6030903.PMID 29722874.
  43. ^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".Bioinformatics.35 (22):4537–4542.doi:10.1093/bioinformatics/btz265.ISSN 1367-4803.PMC 6853651.PMID 31329826.
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