An efficient method for significant motifs discovery from multiple DNA sequences

Abstract

Identification of transcription factor binding sites or biological motifs is an important step in deciphering the mechanisms of gene regulation. It is a classic problem that has eluded a satisfactory and efficient solution. In this paper, we devise a three-phase algorithm to mine for biologically significant motifs. In the first phase, we generate all the possible string motifs, this phase is followed by a filtering process where we discard all motifs that do not meet the constraints. And in the final phase, motifs are scored and ranked using a combination of stochastic techniques and [Formula: see text]-value. We show that our method outperforms some very well-known motif discovery tools, e.g. MEME and Weeder on well-established benchmark data suites. We also apply the algorithm on the non-coding regions of M. tuberculosis and report significant motifs of size 10 with excellent [Formula: see text]-values in a fraction of the time MEME and MoSDi did. In fact, among the best 10 motifs ([Formula: see text]-value wise) in the non-coding regions of M. tuberculosis reported by the tools MEME, MoSDi and ours, five were discovered by our approach which included the third and the fourth best ones. All this in 1/17 and 1/6 the time which MEME and MoSDi (respectively) took.