This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison