SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
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- dc.contributor.author Mariotti, Marco, 1984-ca
- dc.contributor.author Lobanov, Alexei V.ca
- dc.contributor.author Guigó Serra, Rodericca
- dc.contributor.author Gladyshev, Vadim N.ca
- dc.date.accessioned 2015-02-06T08:10:02Z
- dc.date.available 2015-02-06T08:10:02Z
- dc.date.issued 2013ca
- dc.description.abstract Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3' UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.
- dc.format.mimetype application/pdfca
- dc.identifier.citation Mariotti M, Lobanov AV, Guigo R, Gladyshev VN. SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins. Nucleic Acids Res. 2013;41(15):e149. DOI: 10.1093/nar/gkt550ca
- dc.identifier.doi http://dx.doi.org/10.1093/nar/gkt550
- dc.identifier.issn 0305-1048ca
- dc.identifier.uri http://hdl.handle.net/10230/23101
- dc.language.iso engca
- dc.publisher Oxford University Pressca
- dc.relation.ispartof Nucleic Acids Research. 2013;41(15):e149
- dc.rights © 2013 Marco Mariotti et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution Non-Commercial License which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly citedca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
- dc.subject.other Biologia computacional
- dc.subject.other Selenoproteïnes
- dc.subject.other Compostos organoselènics
- dc.title SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteinsca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca