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