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• W2588893359 endingPage "e1005383" @default.
• W2588893359 startingPage "e1005383" @default.
• W2588893359 abstract "Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat." @default.
• W2588893359 created "2017-02-24" @default.
• W2588893359 creator A5008294547 @default.
• W2588893359 creator A5067701434 @default.
• W2588893359 creator A5082613226 @default.
• W2588893359 date "2017-02-13" @default.
• W2588893359 modified "2023-10-09" @default.
• W2588893359 title "Computational identification of the selenocysteine tRNA (tRNASec) in genomes" @default.
• W2588893359 cites W1482179078 @default.
• W2588893359 cites W1572640010 @default.
• W2588893359 cites W1583414424 @default.
• W2588893359 cites W1641384127 @default.
• W2588893359 cites W1965510337 @default.
• W2588893359 cites W1966413612 @default.
• W2588893359 cites W1973290333 @default.
• W2588893359 cites W1981933894 @default.
• W2588893359 cites W1985743388 @default.
• W2588893359 cites W1985970087 @default.
• W2588893359 cites W1989606632 @default.
• W2588893359 cites W1993334394 @default.
• W2588893359 cites W1996053875 @default.
• W2588893359 cites W2001415595 @default.
• W2588893359 cites W2008139174 @default.
• W2588893359 cites W2008417944 @default.
• W2588893359 cites W2017638348 @default.
• W2588893359 cites W2025121505 @default.
• W2588893359 cites W2026393494 @default.
• W2588893359 cites W2032464327 @default.
• W2588893359 cites W2039618870 @default.
• W2588893359 cites W2050008018 @default.
• W2588893359 cites W2050289674 @default.
• W2588893359 cites W2060357981 @default.
• W2588893359 cites W2067781507 @default.
• W2588893359 cites W2068117645 @default.
• W2588893359 cites W2076992251 @default.
• W2588893359 cites W2079556709 @default.
• W2588893359 cites W2080388275 @default.
• W2588893359 cites W2084389954 @default.
• W2588893359 cites W2086561953 @default.
• W2588893359 cites W2087724791 @default.
• W2588893359 cites W2089600895 @default.
• W2588893359 cites W2090811420 @default.
• W2588893359 cites W2096173332 @default.
• W2588893359 cites W2097637665 @default.
• W2588893359 cites W2098890352 @default.
• W2588893359 cites W2103848900 @default.
• W2588893359 cites W2104620517 @default.
• W2588893359 cites W2108230379 @default.
• W2588893359 cites W2108770512 @default.
• W2588893359 cites W2110593787 @default.
• W2588893359 cites W2115537066 @default.
• W2588893359 cites W2115560639 @default.
• W2588893359 cites W2118059471 @default.
• W2588893359 cites W2120965099 @default.
• W2588893359 cites W2123940707 @default.
• W2588893359 cites W2124108929 @default.
• W2588893359 cites W2125858402 @default.
• W2588893359 cites W2128016314 @default.
• W2588893359 cites W2128360087 @default.
• W2588893359 cites W2133919074 @default.
• W2588893359 cites W2136018175 @default.
• W2588893359 cites W2139952582 @default.
• W2588893359 cites W2141152740 @default.
• W2588893359 cites W2141947101 @default.
• W2588893359 cites W2146307110 @default.
• W2588893359 cites W2147718959 @default.
• W2588893359 cites W2149005038 @default.
• W2588893359 cites W2149427179 @default.
• W2588893359 cites W2149429041 @default.
• W2588893359 cites W2158096004 @default.
• W2588893359 cites W2158266834 @default.
• W2588893359 cites W2158714788 @default.
• W2588893359 cites W2165072468 @default.
• W2588893359 cites W2165423242 @default.
• W2588893359 cites W2172183886 @default.
• W2588893359 cites W2194949096 @default.
• W2588893359 cites W2300560013 @default.
• W2588893359 cites W2473079737 @default.
• W2588893359 cites W2528348387 @default.
• W2588893359 cites W2529529221 @default.
• W2588893359 cites W2550234534 @default.
• W2588893359 cites W319682455 @default.
• W2588893359 cites W4246174145 @default.
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• W2588893359 doi "https://doi.org/10.1371/journal.pcbi.1005383" @default.
• W2588893359 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5330540" @default.
• W2588893359 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/28192430" @default.
• W2588893359 hasPublicationYear "2017" @default.
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