catRAPID omics: a web server for large-scale prediction of protein-RNA interactions
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- dc.contributor.author Agostini, Federico, 1985-ca
- dc.contributor.author Zanzoni, Andreasca
- dc.contributor.author Klus, Petr, 1985-ca
- dc.contributor.author Marchese, Domenica, 1986-ca
- dc.contributor.author Cirillo, Davideca
- dc.contributor.author Tartaglia, Gian Gaetanoca
- dc.date.accessioned 2014-06-03T07:23:35Z
- dc.date.available 2014-06-03T07:23:35Z
- dc.date.issued 2013ca
- dc.description.abstract SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition. RESULTS: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3'-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation./nAVAILABILITY: catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group.
- dc.description.sponsorship Funding: Spanish Ministry of Economy and Competitiveness (SAF2011-26211), the European Research Council (ERC Starting Grant to G.G.T) and the RTTIC project (to A.Z.). ‘La Caixa’ fellowship (to P.K.). Programa de Ayudas FPI del Ministerio de Economia y Competitividad—BES-2012-052457 (to D.M.)
- dc.format.mimetype application/pdfca
- dc.identifier.citation Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics. 2013;29(22):2928-30. DOI: 10.1093/bioinformatics/btt495ca
- dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btt495
- dc.identifier.issn 1367-4803ca
- dc.identifier.uri http://hdl.handle.net/10230/22554
- dc.language.iso engca
- dc.publisher Oxford University Pressca
- dc.relation.ispartof Bioinformatics. 2013;29(22):2928-30
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545ca
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2011-26211
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BES2012-052457
- dc.rights © Federico Agostini et al 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License, which permits unrestricted reuse, 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/3.0/
- dc.subject.other RNA
- dc.subject.other Proteïnes
- dc.subject.other Programes d'ordinador
- dc.title catRAPID omics: a web server for large-scale prediction of protein-RNA interactionsca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca