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Exploring the Space of Consensus RNA Secondary Structure Motifs Using Suffix Arrays

In the last few years, we have seen a rapid increase of the number of known RNA families. For a significant fraction of them, the mechanisms of action remain unclear. Their signature combines structure and sequence information. In most cases, they are difficult to identify from sequence alone. Traditional approaches to identify RNA motifs seek to find a conserved structure with minimum free energy in an ensemble of aligned sequences. We present a novel approach for discovering consensus secondary structure motifs in a set of unaligned RNA sequences. The secondary structure motifs combine sequence and structure information. State-of-the-art data structures, suffix arrays in particular, are used to enumerate exhaustively the space of possible motifs. Suffix arrays (SAs) are used for two purposes. First, to enumerate efficiently stem structures, including internal loops. Second, SAs are used to match secondary structure expressions. The algorithms have been implemented in a software system called Seed. Applications of the approach on test cases shows that i) complex search spaces can be exhaustively explored and that ii) the search spaces contains biologically relevant candidates.