{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T18:56:37Z","timestamp":1778871397129,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1428,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Frameshift (FS) prediction is important for analysis and biological interpretation of metagenomic sequences. Since a genomic context of a short metagenomic sequence is rarely known, there is not enough data available to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. The challenge of ab initio FS detection is, therefore, two fold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). Here we describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It is shown on multiple test sets that the MetaGeneTack FS detection performance is comparable or better than the one of earlier developed program FragGeneScan.<\/jats:p>\n               <jats:p>Availability and implementation: MetaGeneTack is available as a web server at http:\/\/exon.gatech.edu\/GeneTack\/cgi\/metagenetack.cgi. Academic users can download a standalone version of the program from http:\/\/exon.gatech.edu\/license_download.cgi.<\/jats:p>\n               <jats:p>Contact: \u00a0borodovsky@gatech.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts636","type":"journal-article","created":{"date-parts":[[2012,11,6]],"date-time":"2012-11-06T03:08:43Z","timestamp":1352171323000},"page":"114-116","source":"Crossref","is-referenced-by-count":16,"title":["MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences"],"prefix":"10.1093","volume":"29","author":[{"given":"Shiyuyun","family":"Tang","sequence":"first","affiliation":[{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan","family":"Antonov","sequence":"additional","affiliation":[{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Borodovsky","sequence":"additional","affiliation":[{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"},{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"},{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"},{"name":"1 School of Biology, 2School of Computational Science and Engineering, 3Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA, 4Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia and 5Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,4]]},"reference":[{"key":"2023020303201055800_bts636-B1","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1142\/S0219720010004847","article-title":"GeneTack: frameshift identification in protein coding sequences by the Viterbi algorithm","volume":"8","author":"Antonov","year":"2010","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023020303201055800_bts636-B2","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023020303201055800_bts636-B3","doi-asserted-by":"crossref","first-page":"3911","DOI":"10.1093\/nar\/27.19.3911","article-title":"Heuristic approach to deriving models for gene finding","volume":"27","author":"Besemer","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023020303201055800_bts636-B4","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1186\/1471-2164-10-520","article-title":"The effect of sequencing errors on metagenomic gene prediction","volume":"10","author":"Hoff","year":"2009","journal-title":"BMC Genomics"},{"key":"2023020303201055800_bts636-B5","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1128\/MMBR.00009-08","article-title":"A bioinformatician\u2019s guide to metagenomics","volume":"72","author":"Kunin","year":"2008","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2023020303201055800_bts636-B7","doi-asserted-by":"crossref","first-page":"e30087","DOI":"10.1371\/journal.pone.0030087","article-title":"Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA samples","volume":"7","author":"Luo","year":"2012","journal-title":"PLoS One"},{"key":"2023020303201055800_bts636-B8","doi-asserted-by":"crossref","first-page":"e191","DOI":"10.1093\/nar\/gkq747","article-title":"FragGeneScan: predicting genes in short and error-prone reads","volume":"38","author":"Rho","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020303201055800_bts636-B9","doi-asserted-by":"crossref","first-page":"e1000667","DOI":"10.1371\/journal.pcbi.1000667","article-title":"A primer on metagenomics","volume":"6","author":"Wooley","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023020303201055800_bts636-B10","doi-asserted-by":"crossref","first-page":"e132","DOI":"10.1093\/nar\/gkq275","article-title":"Ab initio gene identification in metagenomic sequences","volume":"38","author":"Zhu","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/114\/49060446\/bioinformatics_29_1_114.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/114\/49060446\/bioinformatics_29_1_114.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T03:21:03Z","timestamp":1675394463000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/1\/114\/272572"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,4]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts636","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1]]},"published":{"date-parts":[[2012,11,4]]}}}