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PMS6MC: A Multicore Algorithm for Motif Discovery

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Author(s): Shibdas Bandyopadhyay | Sartaj Sahni | Sanguthevar Rajasekaran

Journal: Algorithms
ISSN 1999-4893

Volume: 6;
Issue: 4;
Start page: 805;
Date: 2013;
Original page

Keywords: planted motif search | parallel string algorithms | multi-core algorithms

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.

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