Multiple alignment and structure prediction of non-coding RNA sequences

This work proposes a novel approach to solve the problem of simultaneous multiple alignment and structure prediction for RNA sequences by combining heuristics for multiple sequences with pairwise implementations.

Abstract

Background As the importance of non-coding RNAs becomes more evident, the need for computational methods for ncRNAs grows. Predicting the secondary structure is of great importance, and combining this with multiple alignment yields a useful tool for researchers. The exact solution to the problem of simultaneous multiple alignment and structure prediction for RNA sequences was described by Sankoff [1], but to date only pairwise implementations (e.g. Foldalign [2], Dynalign [3]) or heuristics for multiple sequences (e.g. FoldalignM [4], LocARNA [5], RNA Sampler [6]) exist.