Parallel Implementation of Exact Algorithm for Planted Motif Search Problem using SMP Cluster

The problem of identifying repeated patterns having biological significance (i.e., motifs) from biological data has been studied extensively due to its paramount importance. Despite extensive studies and research, the motif finding problem still remains a challenge. Most of the sequential motif finding algorithms contains lots of repeated, data-independent operations. In this paper, the authors propose an improvement over the existing exact planted (l, d) motif search algorithm developed by Rajsekharan et. al. using a bit-vector mapping technique to avoid sorting and merging among huge number of l -mers generated by different sequences. They also develop a parallel algorithm for this modified sequential algorithm.

Provided by: EuroJournals Topic: Software Date Added: Nov 2011 Format: PDF

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