PT  - JOURNAL ARTICLE
AU  - Riccardo Delli Ponti
AU  - Alexandros Armaos
AU  - Gian Gaetano Tartaglia
TI  - <em>CROSSalive</em>: a web server for predicting the <em>in vivo</em> structure of RNA molecules
AID  - 10.1101/626085
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 626085
4099  - http://biorxiv.org/content/early/2019/05/11/626085.short
4100  - http://biorxiv.org/content/early/2019/05/11/626085.full
AB  - Here we introduce CROSSalive, an algorithm to predict the RNA secondary structure profile (double and single stranded regions) in vivo and without sequence length limitations. Using predictions of protein interactions CROSSalive predicts the effect of N6 adenosine methylation (m6a) on RNA structure. Trained on icSHAPE data in presence (m6a+) and absence (m6a-) of methylation CROSSalive achieves an accuracy of 0.88 on the test set. The algorithm was also applied to the murine long non-coding RNA Xist (17900 nt, not present in the training) and shows a Pearson’s correlation of 0.45 with SHAPE-map data. CROSSalive webserver is freely accessible at the following page: http://service.tartaglialab.com/new_submission/crossalive