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dc.contributor.authorSantesmasses, Didacen_US
dc.contributor.authorMariotti, Marcoen_US
dc.contributor.authorGuigó, Rodericen_US
dc.date.accessioned2017-04-06T03:18:52Z
dc.date.issued2017en_US
dc.identifier.citationSantesmasses, Didac, Marco Mariotti, and Roderic Guigó. 2017. “Computational identification of the selenocysteine tRNA (tRNASec) in genomes.” PLoS Computational Biology 13 (2): e1005383. doi:10.1371/journal.pcbi.1005383. http://dx.doi.org/10.1371/journal.pcbi.1005383.en
dc.identifier.issnen
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:32071997
dc.description.abstractSelenocysteine (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.en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.relation.isversionofdoi:10.1371/journal.pcbi.1005383en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330540/pdf/en
dash.licenseLAAen_US
dc.subjectBiology and life sciencesen
dc.subjectBiochemistryen
dc.subjectNucleic acidsen
dc.subjectRNAen
dc.subjectNon-coding RNAen
dc.subjectTransfer RNAen
dc.subjectBiology and Life Sciencesen
dc.subjectGeneticsen
dc.subjectGenomicsen
dc.subjectAnimal Genomicsen
dc.subjectInvertebrate Genomicsen
dc.subjectDatabase and Informatics Methodsen
dc.subjectBioinformaticsen
dc.subjectSequence Analysisen
dc.subjectSequence Alignmenten
dc.subjectFungal Geneticsen
dc.subjectFungal Genomicsen
dc.subjectMycologyen
dc.subjectBiological Databasesen
dc.subjectGenomic Databasesen
dc.subjectComputational Biologyen
dc.subjectGenome Analysisen
dc.subjectMicrobiologyen
dc.subjectArchaean Biologyen
dc.subjectGene Predictionen
dc.subjectComputational Techniquesen
dc.subjectSplit-Decomposition Methoden
dc.subjectMultiple Alignment Calculationen
dc.titleComputational identification of the selenocysteine tRNA (tRNASec) in genomesen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalPLoS Computational Biologyen
dash.depositing.authorMariotti, Marcoen_US
dc.date.available2017-04-06T03:18:52Z
dc.identifier.doi10.1371/journal.pcbi.1005383*
dash.contributor.affiliatedMariotti, Marco


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