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Algorithms 2013, 6(4), 805-823; doi:10.3390/a6040805
Article

PMS6MC: A Multicore Algorithm for Motif Discovery

1,* , 2
 and
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 / Revised: 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 planted motif search; parallel string algorithms; multi-core algorithms
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Bandyopadhyay, S.; Sahni, S.; Rajasekaran, S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms 2013, 6, 805-823.

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