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

摘要：

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).

关键词： sequence alignment Smith-Waterman cell broadband engine SSE2 SIMD MIMD GPU

作者: Nim Tri Hieu Kwoh Chee Keong Adrianto Wirawan Bertil Schmidt

作者单位: Nanyang Technological University, Singapore University of New South Wales Asia

会议类型: 国际会议

会议名称: The 2nd International Conference on Bioinformatics and Biomedical Engineering(iCBBE 2008)(第二届生物信息与生物医学工程国际会议)

会议地点: 上海

会议语种:英文

页码: 5-8

在线出版日期: 2008-05-16（万方平台首次上网日期，不代表论文的发表时间）