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Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes

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dc.contributor.author Mariotti, Marco, 1984-
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2015-07-24T10:10:14Z
dc.date.available 2015-07-24T10:10:14Z
dc.date.issued 2010
dc.identifier.citation Mariotti M, Guigó R. Selenoprofiles: profile-based scanning of eukaryotic/ngenome sequences for selenoprotein genes. Bioinformatics. 2010 Nov 1;26(21):2656-63. DOI: 10.1093/bioinformatics/btq516
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10230/24639
dc.description.abstract MOTIVATION: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases. RESULTS: We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queries to scan genomic sequences. Results of the scan are processed through a number of steps, to produce highly accurate predictions of selenoprotein genes with little or no human intervention. Selenoprofiles is a valuable tool for bioinformatic characterization of eukaryotic selenoproteomes, and can complement genome annotation pipelines. AVAILABILITY AND IMPLEMENTATION: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. The program is available at http://big.crg.cat/services/selenoprofiles. The predictions presented in this article are available through DAS at http://genome.crg.cat:9000/das/Selenoprofiles_ensembl.
dc.description.sponsorship This work was supported by the Spanish Ministerio de Educacion y Ciencia (grant BIO2006-03380); National Institutes of Health/National Human Genome Research Institute (grant 1U54HG004555)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.rights © M. Mariotti and R. Guigó 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.5
dc.subject.other Genomes
dc.subject.other Selenoproteïnes
dc.subject.other Genètica
dc.title Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btq516
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2006-03380
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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