Pampa: An Improved Branch and Bound Algorithm for Planted (l, d) Motif Search

Abstract

Abstract. We consider the planted (l, d) motif search problem as defined in [1] and [12], a problem that arises from the need to find transcription factor-binding sites in genomic information. We build an exact branch and bound algorithm, which has small space requirements. An implementation of this algorithm is able to tackle challenging instances as big as (19, 7), cutting by half the time required by the best existing algorithm