Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications

This paper evaluates the performance of bioinformatics applications on the Cell Broadband Engine recently developed at IBM. In particular we focus on two highly popular bioinformatics applications - FASTA and ClustalW. 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 processing platform. The price and power advantages afforded by the Cell 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.