Limits...
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
Sequence alignment of YPKIEAIY and MPKIIEAIYEN. An example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix[13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW-HE and AWGHE.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2571991&req=5

Figure 1: Sequence alignment of YPKIEAIY and MPKIIEAIYEN. An example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix[13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW-HE and AWGHE.

Mentions: Figure 1 illustrates an example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix [13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW- HE and AWGHE.


CBESW: sequence alignment on the Playstation 3.

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

Sequence alignment of YPKIEAIY and MPKIIEAIYEN. An example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix[13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW-HE and AWGHE.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Sequence alignment of YPKIEAIY and MPKIIEAIYEN. An example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix[13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW-HE and AWGHE.
Mentions: Figure 1 illustrates an example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix [13]. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW- HE and AWGHE.

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