Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine

Authors:
Adrianto Wirawan;Bertil Schmidt;Chee Keong Kwoh
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore, 639798;School of Computer Engineering, Nanyang Technological University, Singapore, 639798;School of Computer Engineering, Nanyang Technological University, Singapore, 639798
Venue:
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
Year:
2009

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Abstract

Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of accelerator technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications compared to general-purpose platforms. In this paper, we demonstrate how the PlayStation®3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the distance matrix computation utilized in multiple sequence alignment algorithms.