SMS-Forbid: An Efficient Agorithm for Simple Motif Problem

Finding common motifs from a set of strings coding biological sequences is an important problem in Molecular Biology. Several versions of the motif finding problem have been proposed in the literature and for each version, numerous algorithms have been developed. However, many of these algorithms fall under the category of heuristics. In this paper, we concentrate on the Simple Motif Problem (SMP) and we propose an exact algorithm, called SMS-Forbid, for this version of motif finding problem. SMS-Forbid make use of less time and space than the known exact algorithms.