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PMS6MC: A Multicore Algorithm for Motif Discovery
VMware Inc, 3401 Hillview Avenue, Palo Alto, CA 94304, USA
Department of CISE, University of Florida, Gainesville, FL 32611, USA
Department of CSE, University of Connecticut, Storrs, CT 06269, USA
* Author to whom correspondence should be addressed.
Received: 15 September 2013; in revised form: 8 November 2013 / Accepted: 11 November 2013 / Published: 18 November 2013
Abstract: We develop an efficient multicore algorithm, PMS6MC, for the (l; d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. PMS6MC is based on PMS6, which is currently the fastest single-core algorithm for motif discovery in large instances. The speedup, relative to PMS6, attained by our multicore algorithm ranges from a high of 6.62 for the (17,6) challenging instances to a low of 2.75 for the (13,4) challenging instances on an Intel 6-core system. We estimate that PMS6MC is 2 to 4 times faster than other parallel algorithms for motif search on large instances.
Keywords: planted motif search; parallel string algorithms; multi-core algorithms
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Bandyopadhyay, S.; Sahni, S.; Rajasekaran, S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms 2013, 6, 805-823.
Bandyopadhyay S, Sahni S, Rajasekaran S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms. 2013; 6(4):805-823.
Bandyopadhyay, Shibdas; Sahni, Sartaj; Rajasekaran, Sanguthevar. 2013. "PMS6MC: A Multicore Algorithm for Motif Discovery." Algorithms 6, no. 4: 805-823.