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omiXcore: a web server for prediction of protein interactions with large RNA

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dc.contributor.author Armaos, Alexandros, 1989-
dc.contributor.author Cirillo, Davide
dc.contributor.author Tartaglia, Gian Gaetano
dc.date.accessioned 2018-08-21T06:18:15Z
dc.date.available 2018-08-21T06:18:15Z
dc.date.issued 2017
dc.identifier.citation Armaos A, Cirillo D, Gaetano Tartaglia G. omiXcore: a web server for prediction of protein interactions with large RNA. Bioinformatics. 2017 Oct 1;33(19):3104-6. DOI: 10.1093/bioinformatics/btx361
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10230/35342
dc.description.abstract SUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites. RESULTS: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation. AVAILABILITY AND IMPLEMENTATION: omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore. CONTACT: gian.tartaglia@crg.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
dc.description.sponsorship We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and the CERCA Programme / Generalitat de Catalunya. This work was supported by the European Union Seventh Framework Programme [FP7/2007-13], European Research Council RIBOMYLOME_309545 (Gian Gaetano Tartaglia) and Spanish Ministry of Economy and Competitiveness BFU2014-5505-P (Gian Gaetano Tartaglia)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Bioinformatics. 2017 Oct 1;33(19):3104-6
dc.rights © Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia 2017. 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/4.0/
dc.subject.other Interaccions RNA-proteïna
dc.subject.other Programes d'ordinador
dc.title omiXcore: a web server for prediction of protein interactions with large RNA
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btx361
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-5505-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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