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

*この研究の対応する著者

研究成果: Article査読

37 被引用数 (Scopus)

抄録

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.

本文言語English
論文番号R16
ジャーナルGenome Biology
15
1
DOI
出版ステータスPublished - 2014
外部発表はい

ASJC Scopus subject areas

  • 生態、進化、行動および分類学
  • 遺伝学
  • 細胞生物学

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