Pairwise distance matrix computation for multiple sequence alignment on the cell broadband engine

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. © 2009 Springer Berlin Heidelberg.