Abstract
In this paper, we present a technique to optimize the performance of database similarity search in the specific context of Cell Broadband Engine Architecture (CBEA). The technique applied was Striped Smith-Waterman algorithm for SIMD and heterogeneous task distribution in MIMD.In terms of sensitivity, the technique preserves the optimality of original Smith- Waterman algorithm. In addition, the performance recorded shows a remarkable speedup of 1.7 to 8.8 folds of this new architecture, as compared to other platforms such as Streaming SIMD Extensions 2 (SSE2) and Graphics Processing Unit (GPU).
Original language | English |
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Title of host publication | Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008) |
Subtitle of host publication | May 16-18, 2008, Shanghai, China |
Publisher | IEEE, Institute of Electrical and Electronics Engineers |
Pages | 5-8 |
Number of pages | 4 |
ISBN (Print) | 9781424417483 |
Publication status | Published - 2008 |
Externally published | Yes |
Event | International Conference on Bioinformatics and Biomedical Engineering 2008 - Shanghai, China Duration: 16 May 2008 → 18 May 2008 Conference number: 2nd |
Conference
Conference | International Conference on Bioinformatics and Biomedical Engineering 2008 |
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Abbreviated title | (iCBBE) |
Country/Territory | China |
City | Shanghai |
Period | 16/05/08 → 18/05/08 |
Keywords
- Sequence alignment
- Smith-Waterman
- cell broadband engine
- SSE2
- SIMD
- MIMD
- GPU