ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs

31.12.2014

Otto C, Möhl M, Heyne S, Amit M, Landau GM, Backofen R, Will S.

BMC Bioinformatics. 2014 Dec 31;15(1):6602.

BMC Bioinformatics.      online article

ExpaRNA-P computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the well-known “simultaneous alignment and folding” of RNAs. ExpaRNA-P's low complexity (quadratic in time and space) is enabled by its novel structure ensemble-based sparsification. We devise a generalized chaining algorithm to compute compatible subsets of ExpaRNA-P’s sequence-structure motifs. Resulting in the very fast RNA alignment approach ExpLoc-P, we utilize the best chain as anchor constraints for the sequence-structure alignment tool LocARNA.