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

Bioinformatics. 2017 Oct 1;33(19):3104-3106. 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.

MeSH terms

  • Binding Sites
  • Humans
  • Internet
  • Protein Binding
  • RNA / chemistry*
  • RNA / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Sequence Analysis, Protein
  • Sequence Analysis, RNA
  • Software*

Substances

  • RNA-Binding Proteins
  • RNA