Capr: Revealing structural specificities of rna-binding protein target recognition using clip-seq data

Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, Hisanori Kiryu

Research output: Contribution to journalArticlepeer-review

37 Citations (Scopus)

Abstract

RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts.

Original languageEnglish
Article numberR16
JournalGenome Biology
Volume15
Issue number1
DOIs
Publication statusPublished - 2014
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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