Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications.” IBM

This paper evaluates the performance of bioinformatics applications on the Cell Broadband Engine (Cell/B.E.) recently developed at IBM. In particular we focus on three highly popular bioinformatics applications – FASTA, ClustalW, and HMMER. The characteristics of these bioinformatics applications, such as small critical time-consuming code size, regular memory accesses, existing vectorized code and embarrassingly parallel computation, make them uniquely suitable for the Cell/B.E. processing platform. The price and power advantages afforded by the Cell/B.E. processor also make it an attractive alternative to general purpose processors. We report preliminary performance results for these applications, and contrast these results with the state-of-the-art hardware. 1 Computational Biology and High-Performance Computing With the discovery of the structure of DNA and the development of new techniques for sequencing the entire genome of organisms, biology is rapidly moving towards a dataintensive, computational science. Biologists search for biomolecular sequence data to compare with other known genomes in order to determine functions and improve understanding of biochemical pathways. Computational biology has been aided by recen