A Simple Algorithm for (l, d) Motif Search1

Extracting meaningful patterns from voluminous amount of biological data is a very big challenge. Motifs are biological patterns of great interest to biologists. There are different versions of the Motif Finding Problem. In this paper we concentrate on the Planted (l, d) Motif Search Problem. There have been numerous algorithms designed to solve this problem. Many instances of the Planted (l, d) Motif Problem have been identified as challenging instances. The algorithm proposed here is an extension of PMS3. It uses a very simple approach and solves challenging instances ((21, 8), for example) that have not been reported solved before in the literature. We also propose a new algorithm PMS3p. We expect PMS3p to be significantly faster than PMS3.