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CBESW: sequence alignment on the Playstation 3.

Wirawan A, Kwoh CK, Hieu NT, Schmidt B - BMC Bioinformatics (2008)

Bottom Line: As a result, the computational power needed by bioinformatics applications is growing exponentially as well.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computer Engineering, Nanyang Technological University, Singapore. adri0004@ntu.edu.sg

ABSTRACT

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.

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Performance comparison with the SSEARCH implementation. Performance comparison between our CBESW implementation with SSEARCH, in terms of MCUPS. All queries were run against Swiss-Prot release 55.2. Nine query sequences with lengths of 63 to 852 amino acids were used.
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Figure 6: Performance comparison with the SSEARCH implementation. Performance comparison between our CBESW implementation with SSEARCH, in terms of MCUPS. All queries were run against Swiss-Prot release 55.2. Nine query sequences with lengths of 63 to 852 amino acids were used.

Mentions: SSEARCH[20] is a SW implementation which is part of the FASTA[21] package. The SSEARCH performance is benchmarked on an Intel Core 2 Duo 2.4 GHz CPU with 1 GB RAM. Both execution cores were used in the experiment. As shown in Figure 6, for a query sequence of length 852 (accession number O60341), SSEARCH achieves a performance of 121.91 MCUPS. Thus, our implementation is over 30 times faster.


CBESW: sequence alignment on the Playstation 3.

Wirawan A, Kwoh CK, Hieu NT, Schmidt B - BMC Bioinformatics (2008)

Performance comparison with the SSEARCH implementation. Performance comparison between our CBESW implementation with SSEARCH, in terms of MCUPS. All queries were run against Swiss-Prot release 55.2. Nine query sequences with lengths of 63 to 852 amino acids were used.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2571991&req=5

Figure 6: Performance comparison with the SSEARCH implementation. Performance comparison between our CBESW implementation with SSEARCH, in terms of MCUPS. All queries were run against Swiss-Prot release 55.2. Nine query sequences with lengths of 63 to 852 amino acids were used.
Mentions: SSEARCH[20] is a SW implementation which is part of the FASTA[21] package. The SSEARCH performance is benchmarked on an Intel Core 2 Duo 2.4 GHz CPU with 1 GB RAM. Both execution cores were used in the experiment. As shown in Figure 6, for a query sequence of length 852 (accession number O60341), SSEARCH achieves a performance of 121.91 MCUPS. Thus, our implementation is over 30 times faster.

Bottom Line: As a result, the computational power needed by bioinformatics applications is growing exponentially as well.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computer Engineering, Nanyang Technological University, Singapore. adri0004@ntu.edu.sg

ABSTRACT

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.

Show MeSH