Recode-2: new design, new search tools, and many more genes
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Published Version
Date
2010
Authors
Bekaert, Michael
Firth, Andrew E.
Zhang, Yan
Gladyshev, Vadim N.
Atkins, John F.
Baranov, Pavel V.
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Published Version
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
Description
Keywords
Ornithine decarboxylase antizyme , Polymerase III holoenzyme , Release factor 2 , Site transfer RNA , Escherichia-coli , Gamma subunit , Transcriptional slippage , Selenoprotein synthesis , Messenger RNAs , Coding gap
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