GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences

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dc.contributor.authorAntonov, Ivan
dc.contributor.authorBaranov, Pavel V.
dc.contributor.authorBorodovsky, Mark
dc.contributor.funderWellcome Trust
dc.contributor.funderNational Institutes of Health
dc.date.accessioned2017-11-14T13:24:30Z
dc.date.available2017-11-14T13:24:30Z
dc.date.issued2013
dc.description.abstractDatabase annotations of prokaryotic genomes and eukaryotic mRNA sequences pay relatively low attention to frame transitions that disrupt protein-coding genes. Frame transitions (frameshifts) could be caused by sequencing errors or indel mutations inside protein-coding regions. Other observed frameshifts are related to recoding events (that evolved to control expression of some genes). Earlier, we have developed an algorithm and software program GeneTack for ab initio frameshift finding in intronless genes. Here, we describe a database (freely available at http://topaz.gatech.edu/GeneTack/db.html) containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (-1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).en
dc.description.sponsorshipNational Institute of Health (HG000783); Wellcome Trust (094423)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationAntonov, I., Baranov, P. and Borodovsky, M. (2013) 'GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences', Nucleic Acids Research, 41(D1), pp. 152-156. doi: 10.1093/nar/gks1062en
dc.identifier.doi10.1093/nar/gks1062
dc.identifier.endpage156
dc.identifier.issn0305-1048
dc.identifier.issuedD1
dc.identifier.journaltitleNucleic Acids Researchen
dc.identifier.startpage152
dc.identifier.urihttps://hdl.handle.net/10468/5020
dc.identifier.volume41
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttps://academic.oup.com/nar/article/41/D1/D152/1055214/GeneTack-database-genes-with-frameshifts-in
dc.rights© 2012, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttps://creativecommons.org/licenses/by-nc/3.0/
dc.subjectCoding sequencesen
dc.subjectExpressionen
dc.subjectNonsenseen
dc.subjectDecayen
dc.subjectIdentificationen
dc.subjectRegionsen
dc.subjectHumansen
dc.subjectErrorsen
dc.subjectPhaseen
dc.titleGeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequencesen
dc.typeArticle (peer-reviewed)en
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