A parallel implementation of the Smith-Waterman algorithm for massive sequences searching

被引：0
|
作者：
Liao, HY [1 ]
Yin, ML [1 ]
Cheng, Y [1 ]
机构：
[1] Calif State Polytech Univ Pomona, Dept Elect & Comp Engn, Pomona, CA 91768 USA
来源：
PROCEEDINGS OF THE 26TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-7 | 2004年 / 26卷
关键词：
biological sequence alignment; massive sequences searching; parallel processing; Smith-Waterman algorithm;
D O I：
暂无
中图分类号：
TP39 [计算机的应用];
学科分类号：
081203 ; 0835 ;
摘要：
Efficient biological sequence searching is an important and challenging task in bioinformatics. Among those fundamental sequence analysis algorithms, the Smith-Waterman algorithm that adopts the dynamic programming mechanism provides very high sensitivity. Unfortunately, the inefficiency in performance of this algorithm limits its applications in the real world. With the advances in the engineering technology, massive parallelism can be achieved using the FPGA(1)-based techniques. In this paper, a parallel implementation methodology of the Smith-Waterman algorithm is presented. This method provides magnificent speedup over the traditional sequential implementation, while maintain the same level of sensitivity.
引用
收藏
页码：2817 / 2820
页数：4
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