Exploring the viability of the Cell Broadband Engine for bioinformatics applications

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.