CBESW: Sequence alignment on the playstation 3

Citations of this article
Mendeley users who have this article in their library.

This artice is free to access.


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. © 2008 Wirawan et al; licensee BioMed Central Ltd.




Wirawan, A., Kwoh, C. K., Hieu, N. T., & Schmidt, B. (2008). CBESW: Sequence alignment on the playstation 3. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-377

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free