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• Sahni, S
• Rajasekaran, S
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Algorithms 2013, 6(4), 805-823; doi:10.3390/a6040805

Article

PMS6MC: A Multicore Algorithm for Motif Discovery

Shibdas Bandyopadhyay ^1,* , Sartaj Sahni ² and Sanguthevar Rajasekaran ³

¹ VMware Inc, 3401 Hillview Avenue, Palo Alto, CA 94304, USA ² Department of CISE, University of Florida, Gainesville, FL 32611, USA ³ 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

(This article belongs to the Special Issue Algorithms for Multi Core Parallel Computation)

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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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