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Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search

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4 Author(s)
Nim Tri Hieu ; Nanyang Technol. Univ., Singapore ; Kwoh Chee Keong ; Adrianto Wirawan ; Bertil Schmidt

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).

Published in:

2008 2nd International Conference on Bioinformatics and Biomedical Engineering

Date of Conference:

16-18 May 2008