An efficient motif finding algorithm for large DNA data sets

Abstract

The planted (l, d) motif discovery has been successfully used to locate transcription factor binding sites in dozens of promoter sequences over the past decade. However, there has not been enough work done in identifying (l, d) motifs in the next-generation sequencing (ChIP-seq) data sets, which contain thousands of input sequences and thereby bring new challenge to make a good identification in reasonable time. To cater this need, we propose a new planted (l, d) motif discovery algorithm named MCES, which identifies motifs by mining and combining emerging substrings. Specially, to handle larger data sets, we design a MapReduce-based strategy to mine emerging substrings distributedly. Experimental results on the simulated data show that i) MCES is able to identify (l, d) motifs efficiently and effectively in thousands to millions of input sequences, and runs faster than the state-of-the-art (l, d) motif discovery algorithms, such as F-motif and TraverStringsR; ii) MCES is able to identify motifs without known lengths, and has a better identification accuracy than the competing algorithm CisFinder. Also, the validity of MCES is tested on real data sets.