1 Sequence Analysis Multi Threaded Vectorized Distance Matrix Computation on the Cell/BE and x86/SSE2 Architectures

Summary: Multiple sequence alignment is an important tool in bioin-formatics. Although efficient heuristic algorithms exist for this prob-lem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this paper, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine (BE), a homogeneous and hetero-geneous multi-core system, respectively. By taking advantage of multiple processors as well as SIMD vectorization, we are able to achieve speedups of two orders of magnitude compared to the pub-licly available implementation utilized in ClustalW. Availability and Implementation: Source codes in C are publicly available a