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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...
We propose a new algorithm, PMS6, 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. The run time ratio PMS5/PMS6, where PMS5 is the fastest previously known algorithm for motif discovery in large instances, ranges from a high of 2.20 for the (21,8) challenge instances to a low of 1...
We extend the fastest comparison based (sample sort) and non-comparison based (radix sort) number sorting algorithms on a GPU to sort large multifield records. Two extensions - direct (the entire record is moved whenever its key is to be moved) and indirect ((key, index) pairs are sorted using the direct extension and then records are ordered according to the obtained index permutation) are discussed...
We consider the sorting of a large number of multifield records on the Cell Broadband engine. We show that our method, which generates runs using a 2-way merge and then merges these runs using a 4-way merge, outperforms previously proposed sort methods that use either comb sort or bitonic sort for run generation followed by a 2-way odd-even merging of runs. Interestingly, best performance is achieved...
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