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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(More)
Organizations in both public and private sectors have become increasingly dependent on electronic data processing. Protecting these important data is of utmost concern to the organizations and cryptography is one of the primary ways to do the job. Public Key Cryptography is used to protect digital data going through an insecure channel from one place to(More)
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,(More)
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(More)
We develop a radix sort algorithm, GRS, suitable to sort multifield records on a graphics processing unit (GPU). We assume the By Field layout for records to be sorted. GRS is benchmarked against the radix sort algorithm, SDK, in NVIDIA's CUDA SDK 3.0 [14] as well as the radix sort algorithm, SRTS, of Merrill and Grimshaw [11]. Although SRTS is faster than(More)