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


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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.esSupplementary information:Supplementary data are available at Bioinformatics online.

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