Recode-2: new design, new search tools, and many more genes

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dc.contributor.author Bekaert, Michael
dc.contributor.author Firth, Andrew E.
dc.contributor.author Zhang, Yan
dc.contributor.author Gladyshev, Vadim N.
dc.contributor.author Atkins, John F.
dc.contributor.author Baranov, Pavel V.
dc.date.accessioned 2017-11-14T13:24:32Z
dc.date.available 2017-11-14T13:24:32Z
dc.date.issued 2010
dc.identifier.citation Bekaert, M., Firth, A. E., Zhang, Y., Gladyshev, V. N., Atkins, J. F. and Baranov, P. V. (2010) 'Recode-2: new design, new search tools, and many more genes', Nucleic Acids Research, 38(D1), pp. 69-74. doi: 10.1093/nar/gkp788 en
dc.identifier.volume 38
dc.identifier.issued D1
dc.identifier.startpage 69
dc.identifier.endpage 74
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/5029
dc.identifier.doi 10.1093/nar/gkp788
dc.description.abstract Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frame-shifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression-a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp788
dc.rights © 2009, 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/2.0/uk/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. en
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.0/uk/
dc.subject Ornithine decarboxylase antizyme en
dc.subject Polymerase III holoenzyme en
dc.subject Release factor 2 en
dc.subject Site transfer RNA en
dc.subject Escherichia-coli en
dc.subject Gamma subunit en
dc.subject Transcriptional slippage en
dc.subject Selenoprotein synthesis en
dc.subject Messenger RNAs en
dc.subject Coding gap en
dc.title Recode-2: new design, new search tools, and many more genes en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Pavel V. Baranov, Biochemistry & Cell Biology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: P.Baranov@ucc.ie en
dc.internal.authorcontactother John F. Atkins, Biochemistry, University College Cork, Cork, Ireland. +353-21-490-3000 Email: j.atkins@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 1290680
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder National Institutes of Health
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress p.baranov@ucc.ie en
dc.internal.IRISemailaddress j.atkins@ucc.ie


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© 2009, 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/2.0/uk/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as © 2009, 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/2.0/uk/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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