High speed homology search using run-time reconfiguration

被引：0
|
作者：
Yamaguchi, Y
Miyajima, Y
Maruyama, T
Konagaya, A
机构：
[1] Univ Tsukuba, Inst Engn Mech & Syst, Tsukuba, Ibaraki 3058573, Japan
[2] Japan Adv Inst Sci & Technol, Ishikawa 9231292, Japan
[3] Japan Riken Genom Sci Ctr, Yokohama, Kanagawa 2300045, Japan
来源：
FIELD-PROGRAMMABLE LOGIC AND APPLICATIONS, PROCEEDINGS: RECONFIGURABLE COMPUTING IS GOING MAINSTREAM | 2002年 / 2438卷
关键词：
D O I：
暂无
中图分类号：
TP301 [理论、方法];
学科分类号：
081202 ;
摘要：
In this paper, we show a new approach for homology search based on run-time reconfiguration. In our approach, the search consists of two phases, and different circuits are configured on demand during the search to make up for the limited memory bandwidth of off-the-shelf FPGA boards. Experiments with an off-the-shelf FPGA (Xilinx XCV2000E) board showed good results. The time for comparing a query sequence of 2,048 elements with a database sequence of 64 million elements by the Smith-Waterman algorithm is about 34 sec, which is about 330 times faster than a desktop computer with a 1GHz Pentium-III.
引用
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页码：281 / 291
页数：11
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