GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
dc.contributor.author | Antonov, Ivan | |
dc.contributor.author | Baranov, Pavel V. | |
dc.contributor.author | Borodovsky, Mark | |
dc.contributor.funder | Wellcome Trust | |
dc.contributor.funder | National Institutes of Health | |
dc.date.accessioned | 2017-11-14T13:24:30Z | |
dc.date.available | 2017-11-14T13:24:30Z | |
dc.date.issued | 2013 | |
dc.description.abstract | Database 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.sponsorship | National Institute of Health (HG000783); Wellcome Trust (094423) | en |
dc.description.status | Peer reviewed | en |
dc.description.version | Published Version | en |
dc.format.mimetype | application/pdf | en |
dc.identifier.citation | Antonov, 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/gks1062 | en |
dc.identifier.doi | 10.1093/nar/gks1062 | |
dc.identifier.endpage | 156 | |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issued | D1 | |
dc.identifier.journaltitle | Nucleic Acids Research | en |
dc.identifier.startpage | 152 | |
dc.identifier.uri | https://hdl.handle.net/10468/5020 | |
dc.identifier.volume | 41 | |
dc.language.iso | en | en |
dc.publisher | Oxford University Press | en |
dc.relation.uri | https://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.uri | https://creativecommons.org/licenses/by-nc/3.0/ | |
dc.subject | Coding sequences | en |
dc.subject | Expression | en |
dc.subject | Nonsense | en |
dc.subject | Decay | en |
dc.subject | Identification | en |
dc.subject | Regions | en |
dc.subject | Humans | en |
dc.subject | Errors | en |
dc.subject | Phase | en |
dc.title | GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences | en |
dc.type | Article (peer-reviewed) | en |
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