An efficient motif search algorithm based on a minimal forbidden patterns approach

Abstract

One of the problems arising in the analysis of biological sequences is the discovery of sequence similarity by finding common motifs. Several versions of the motif finding problem have been proposed for dealing with this problem and for each version, numerous algorithms have been developed. In this paper, we propose an exact algorithm, called SMS-H-Forbid to solve the Simple Motif Problem (SMP). SMS-H-Forbid is based on clever techniques reducing the number of patterns to be searched for. These techniques are fundamentally different from the ones employed in the literature making SMP more practical. © 2011 Springer-Verlag Berlin Heidelberg.