EMS3: An Improved Algorithm for Finding Edit-Distance Based Motifs.

Abstract

Discovering patterns in biological sequences is a crucial step to extract useful information from them. Motifs can be viewed as patterns that occur exactly or with minor changes across some or all of the biological sequences. Motif search has numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity among families of proteins, etc. The general problem of motif search is intractable. One of the most studied models of motif search proposed in literature is Edit-distance based Motif Search (EMS). In EMS, the goal is to find all the patterns of length l that occur with an edit-distance of at most d in each of the input sequences. EMS algorithms existing in the literature do not scale well on challenging instances and large datasets. In this paper, the current state-of-the-art EMS solver is advanced by exploiting the idea of dimension reduction. A novel idea to reduce the cardinality of the alphabet is proposed. The algorithm we propose, EMS3, is an exact algorithm. I.e., it finds all the motifs present in the input sequences. EMS3 can be also viewed as a divide and conquer algorithm. In this paper, we provide theoretical analyses to establish the efficiency of EMS3. Extensive experiments on standard benchmark datasets (synthetic and real-world) show that the proposed algorithm outperforms the existing state-of-the-art algorithm (EMS2).