CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.
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.
Tsukasa
T
Fukunaga
Haruka
H
Ozaki
Goro
G
Terai
Kiyoshi
K
Asai
Wataru
W
Iwasaki
Hisanori
H
Kiryu
D000465:Algorithms; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology; D030541:Databases, Genetic; D006801:Humans; D047468:Immunoprecipitation; D051379:Mice; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
D016601:RNA-Binding Proteins