GPU accelerated Smith-Waterman

被引：0
|
作者：
Liu, Yang [1 ]
Huang, Wayne [1 ]
Johnson, John [1 ]
Vaidya, Sheila [1 ]
机构：
[1] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA
来源：
COMPUTATIONAL SCIENCE - ICCS 2006, PT 4, PROCEEDINGS | 2006年 / 3994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：
We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonstrate that our system's performance is competitive with current optimized software packages.
引用
收藏
页码：188 / 195
页数：8
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