Finding Common Sequence and Structure Motifs in a set of RNA Sequences

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pair-wise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pair-wise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.