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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
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 planted motif search; parallel string algorithms; multi-core algorithms
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Bandyopadhyay, S.; Sahni, S.; Rajasekaran, S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms 2013, 6, 805-823.

AMA Style

Bandyopadhyay S, Sahni S, Rajasekaran S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms. 2013; 6(4):805-823.

Chicago/Turabian Style

Bandyopadhyay, Shibdas; Sahni, Sartaj; Rajasekaran, Sanguthevar. 2013. "PMS6MC: A Multicore Algorithm for Motif Discovery." Algorithms 6, no. 4: 805-823.

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