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

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• dc.contributor.author Mariotti, Marco, 1984-ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.date.accessioned 2015-07-24T10:10:14Z
• dc.date.available 2015-07-24T10:10:14Z
• dc.date.issued 2010ca
• 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/pdfca
• 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/btq516ca
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btq516
• dc.identifier.issn 1367-4803ca
• dc.identifier.uri http://hdl.handle.net/10230/24639
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Bioinformatics. 2010 Nov 1;26(21):2656-63
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2006-03380
• 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 Licenseca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• 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 genesca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca