BACKGROUND: The exponential growth of available biological data has caused 
bioinformatics to be rapidly moving towards a data-intensive, computational 
science. As a result, the computational power needed by bioinformatics 
applications is growing exponentially as well. The recent emergence of 
accelerator technologies has made it possible to achieve an excellent 
improvement in execution time for many bioinformatics applications, compared to 
current general-purpose platforms. In this paper, we demonstrate how the 
PlayStation 3, powered by the Cell Broadband Engine, can be used as a 
computational platform to accelerate the Smith-Waterman algorithm.
RESULTS: For large datasets, our implementation on the PlayStation 3 provides a 
significant improvement in running time compared to other implementations such 
as SSEARCH, Striped Smith-Waterman and CUDA. Our implementation achieves a peak 
performance of up to 3,646 MCUPS.
CONCLUSION: The results from our experiments demonstrate that the PlayStation 3 
console can be used as an efficient low cost computational platform for high 
performance sequence alignment applications.