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omiXcore: a web server for prediction of protein interactions with large RNA
Alexandros Armaos1,2, Davide Cirillo1,2, Gian Gaetano Tartaglia1,2,3
1Bioinformatics and Genomics, Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology.
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.
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