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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.

Show MeSH
Block diagram of the Cell BE Architecture. The Cell BE architecture consists of 1 PPE and 8 SPEs. However, in the Play Station® 3, only 6 SPEs are available.
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Figure 2: Block diagram of the Cell BE Architecture. The Cell BE architecture consists of 1 PPE and 8 SPEs. However, in the Play Station® 3, only 6 SPEs are available.

Mentions: The Cell BE combines an IBM PowerPC Processor Element (PPE) and eight Synergistic Processor Elements (SPEs)[11]. An integrated high-bandwidth bus called the Element Interconnect Bus (EIB) connects the processors and their ports to external memory and I/O devices. The block diagram of the Cell BE architecture is shown in Figure 2.


CBESW: sequence alignment on the Playstation 3.

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

Block diagram of the Cell BE Architecture. The Cell BE architecture consists of 1 PPE and 8 SPEs. However, in the Play Station® 3, only 6 SPEs are available.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Block diagram of the Cell BE Architecture. The Cell BE architecture consists of 1 PPE and 8 SPEs. However, in the Play Station® 3, only 6 SPEs are available.
Mentions: The Cell BE combines an IBM PowerPC Processor Element (PPE) and eight Synergistic Processor Elements (SPEs)[11]. An integrated high-bandwidth bus called the Element Interconnect Bus (EIB) connects the processors and their ports to external memory and I/O devices. The block diagram of the Cell BE architecture is shown in Figure 2.

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