Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search

Hieu Tri Nim, Chee Keong Kwoh, Adrianto Wirawan, Bertil Schmidt

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearch

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 languageEnglish
Title of host publicationProceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008)
Subtitle of host publicationMay 16-18, 2008, Shanghai, China
PublisherIEEE, Institute of Electrical and Electronics Engineers
Pages5-8
Number of pages4
ISBN (Print)9781424417483
Publication statusPublished - 2008
Externally publishedYes
EventInternational Conference on Bioinformatics and Biomedical Engineering 2008 - Shanghai, China
Duration: 16 May 200818 May 2008
Conference number: 2nd

Conference

ConferenceInternational Conference on Bioinformatics and Biomedical Engineering 2008
Abbreviated title(iCBBE)
CountryChina
CityShanghai
Period16/05/0818/05/08

Keywords

  • Sequence alignment
  • Smith-Waterman
  • cell broadband engine
  • SSE2
  • SIMD
  • MIMD
  • GPU

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