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

Armaos, Alexandros, 1989-; Cirillo, Davide; Tartaglia, Gian Gaetano

doi:http://dx.doi.org/10.1093/bioinformatics/btx361

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

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Citation

Armaos A, Cirillo D, Gaetano Tartaglia G. omiXcore: a web server for prediction of protein interactions with large RNA. Bioinformatics. 2017 Oct 1;33(19):3104-6. DOI: 10.1093/bioinformatics/btx361

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.