Optimizing Performance, Cost, and Sensitivity in Pairwise Sequence Search on a Cluster of PlayStations

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Executive Summary

The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadratic time and space complexity. As a result, many algorithmic and architectural enhancements have been proposed to solve this problem, but at the cost of reduced sensitivity in the algorithms or significant expense in hardware, respectively. This paper presents a highly efficient parallelization of the Smith-Waterman algorithm on the Cell Broadband Engine platform, a novel hybrid multicore architecture that drives the low-cost PlayStation 3 (PS3) game consoles as well as the IBM BladeCenter Q22, which currently powers the fastest supercomputer in the world, Roadrunner at Los Alamos National Laboratory.

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