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Bioinformatics. 2017 Oct 1;33(19):3104-3106. doi: 10.1093/bioinformatics/btx361.

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

Author information

1
Bioinformatics and Genomics, Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology.
2
Bioinformatics and Genomics, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
3
Bioinformatics and Genomics, Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.

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.

PMID:
28637296
PMCID:
PMC5870566
DOI:
10.1093/bioinformatics/btx361
[Indexed for MEDLINE]
Free PMC Article

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