CROSSalive: a web server for predicting the in vivo structure of RNA molecules

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• dc.contributor.author Delli Ponti, Riccardo, 1987-
• dc.contributor.author Armaos, Alexandros, 1989-
• dc.contributor.author Vandelli, Andrea
• dc.contributor.author Tartaglia, Gian Gaetano
• dc.date.accessioned 2020-03-17T07:33:32Z
• dc.date.available 2020-03-17T07:33:32Z
• dc.date.issued 2020
• dc.description.abstract MOTIVATION: RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and double-stranded regions of RNAs in vivo using predictions of protein interactions. RESULTS: Trained on icSHAPE data in presence (m6a+) and absence of N6 methyladenosine modification (m6a-), CROSSalive achieves cross-validation accuracies between 0.70 and 0.88 in identifying high-confidence single- and double-stranded regions. The algorithm was applied to the long non-coding RNA Xist (17 900 nt, not present in the training) and shows an Area under the ROC curve of 0.83 in predicting structured regions. AVAILABILITY AND IMPLEMENTATION: CROSSalive webserver is freely accessible at http://service.tartaglialab.com/new_submission/crossalive. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
• dc.description.sponsorship The research leading to these results has received funding from European Research Council RIBOMYLOME_309545, European Union's Horizon 2020 IASIS_727658 and INFORE_825070, as well as Spanish Ministry of Economy and Competitiveness BFU2017-86970-P
• dc.format.mimetype application/pdf
• dc.identifier.citation Ponti RD, Armaos A, Vandelli A, Tartaglia GG. CROSSalive: a web server for predicting the in vivo structure of RNA molecules. Bioinformatics. 2020 Feb 1; 36(3): 940-941. DOI: 10.1093/bioinformatics/btz666
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btz666
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/43907
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2020 Feb 1; 36(3): 940-1
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/727658
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825070
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86970-P
• dc.rights © 2019 Riccardo Delli Ponti et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Interaccions RNA-proteïna
• dc.subject.other Molècules
• dc.subject.other Servidors web
• dc.title CROSSalive: a web server for predicting the in vivo structure of RNA molecules
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion