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

Delli Ponti, Riccardo, 1987-; Armaos, Alexandros, 1989-; Vandelli, Andrea; Tartaglia, Gian Gaetano

doi:http://dx.doi.org/10.1093/bioinformatics/btz666

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

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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

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.