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CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

Tsukasa Fukunaga1*, Haruka Ozaki1, Goro Terai2, Kiyoshi Asai13, Wataru Iwasaki14 and Hisanori Kiryu1

Author Affiliations

1 Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8568, Japan

2 INTEC Inc, 1-3-3 Shinsuna Koto-ku, Tokyo 136-8637, Japan

3 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan

4 Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan

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Genome Biology 2014, 15:R16  doi:10.1186/gb-2014-15-1-r16

Published: 21 January 2014

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. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr webcite.