An efficient multicore implementation of planted motif problem

In this paper we propose a parallel algorithm for the planted motif problem that arises in computational biology. A variety of algorithms have been proposed in the literature to solve this problem. The drawback of all these algorithms is that they have been designed to work on serial computers; and are not suitable for parallelization on current multicore architectures. We have implemented the proposed algorithm on a 4 Quad-Core Intel Xeon X5550 2.67GHz processor for a total of 16 cores. We compare our performance results with the best performance results reported in the literature; and showed that the performance of our algorithm scales linearly with the number of cores. We also solved the (21, 8) challenging instance on 16 cores in 6.9 hrs.