omiXcore: a web server for prediction of protein interactions with large RNA

Abstract

SUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites. RESULTS: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation. AVAILABILITY AND IMPLEMENTATION: omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore. CONTACT: gian.tartaglia@crg.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.