Jan Gorodkin, Laurie J. Heyer, and Gary D. Stormo
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.