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Updated: Jan 19, 2026
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
CROSSalive: a web server for predicting the in vivo structure of RNA molecules
Riccardo Delli Ponti1,2, Alexandros Armaos1,2, Andrea Vandelli1,2
1Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.
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.
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