Efficient BSP/CGM Algorithms for the Maximum Subsequence Sum and Related Problems 1

Abstract

Abstract Given a sequence of n numbers, with at least one positive value, the maximum subsequence sum problem consists in finding the contiguous subsequence with the largest sum or score, among all derived subsequences of the original sequence. Several scientific applications have used algorithms that solve the maximum subsequence sum. Particularly in Computational Biology, these algorithms can help in the tasks of identification of transmembrane domains and in the search for GC -content regions, a required activity in the operation of pathogenicity islands location. The sequential algorithm that solves this problem has Otn) time complexity. In this work we present BSP/CGM parallel algorithms to solve the maximum subsequence sum problem and three related problems: the maximum longest subsequence sum, the maximum shortest subsequence sum and the number of disjoints subsequences of maximum sum. To the best of our knowledge there are no parallel BSP/CGM algorithms for these related problems. Our algorithms use p processors and require Otn/p) parallel time with a constant number of communication rounds for the algorithm of the maximum subsequence sum and Otlog p) communication rounds, with Otn/p) local computation per round, for the algorithm of the related problems. We implemented the algorithms on a cluster of computers using MPI and on a machine with GPU using CUDA, both with good speed-ups.