We develop an efficient multicore algorithm, PMS6MC, for the (l, d)-motif\r\ndiscovery problem in which we are to find all strings of length l that appear in every string\r\nof a given set of strings with at most d mismatches. PMS6MC is based on PMS6, which\r\nis currently the fastest single-core algorithm for motif discovery in large instances. The\r\nspeedup, relative to PMS6, attained by our multicore algorithm ranges from a high of 6.62\r\nfor the (17,6) challenging instances to a low of 2.75 for the (13,4) challenging instances on\r\nan Intel 6-core system. We estimate that PMS6MC is 2 to 4 times faster than other parallel\r\nalgorithms for motif search on large instances.
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