catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

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• dc.contributor.author Livi, Carmen Mariaca
• dc.contributor.author Klus, Petr, 1985-ca
• dc.contributor.author Delli Ponti, Riccardo, 1987-ca
• dc.contributor.author Tartaglia, Gian Gaetanoca
• dc.date.accessioned 2016-06-01T12:58:43Z
• dc.date.available 2016-06-01T12:58:43Z
• dc.date.issued 2016
• dc.description.abstract MOTIVATION: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets. AVAILABILITY AND IMPLEMENTATION: catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signatureca
• dc.description.sponsorship The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement nº RIBOMYLOME_309545. We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and FEDER funds (European Regional Development Fund) under the project number BFU2014-55054-P. R. Delli Ponti is supported by the MINECO’s pre-doctoral grant Severo Ochoa 2013–2017 (SVP-2014-068402).
• dc.format.mimetype application/pdfca
• dc.identifier.citation Livi CM, Klus P, Delli Ponti R, Tartaglia GG. catRAPID signature: identification of ribonucleoproteins and RNA-binding regions. Bioinformatics. 2016; 32(5): 773-775. DOI 10.1093/bioinformatics/btv629ca
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btv629
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/26792
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Bioinformatics. 2016; 32(5): 773-775
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV-2012-0208
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SVP-2014-068402
• dc.rights © The Author 2015. Published by Oxford University Press./nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), 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/4.0/ca
• dc.subject.other RNAca
• dc.title catRAPID signature: identification of ribonucleoproteins and RNA-binding regionsca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca