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  • 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. We implemented our efficient algorithm as software named ‘CapR’, which can compute the structural profiles for tens of thousands of long RNAs within a reasonable time by enumerating all the possible secondary structures of the RNAs. In this study, we developed an efficient algorithm that calculates the structural profiles of RNAs, and implemented it as CapR. The algorithm was implemented as software named CapR and was applied to the CLIP-seq data of various RBPs. We implemented the algorithms in C++ as a program named CapR.
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