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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.

SUBMITTER: Armaos A

PROVIDER: S-EPMC5870566 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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

Armaos Alexandros A Cirillo Davide D Gaetano Tartaglia Gian G

Bioinformatics (Oxford, England) 20171001 19

<h4>Summary</h4>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.<h4>Results</h4>omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting ...[more]

PMID: 28637296

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