CBESWdemonstrates how the PlayStation® 3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the Smith-Waterman algorithm. It also demonstrates that the PlayStation® 3 console can be used as an efficient low cost computational platform for high performance sequence alignment applications.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. CBESW achieves a peak performance of up to 3.646 GCUPS. This performance is about 30x faster than the straightforward C-implementation in SSEARCH. It is also 1.64x faster than the highly optimized striped SW implementation on an Intel processor and 3x times faster than a CUDA implementation on an Nvidia GeForce 8800GTX.
- PlayStation® 3
- Yellow Dog Linux
- Cell SDK 2.0
:: MORE INFORMATION
Adrianto Wirawan, Chee Keong Kwoh, Tri Hieu Nim, Bertil Schmidt:
“CBESW: Sequence Alignment on the Playstation 3“.
BMC Bioinformatics, 2008, 9:377