Delli Ponti, Riccardo, 1987-Armaos, Alexandros, 1989-Vandelli, AndreaTartaglia, Gian Gaetano2020-03-172020-03-172020Ponti 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/btz6661367-4803http://hdl.handle.net/10230/43907MOTIVATION: 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.application/pdfeng© 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 citedInteraccions RNA-proteïnaMolèculesServidors webinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bioinformatics/btz666info:eu-repo/semantics/openAccess