An Efficient and High Performance Linear Recursive Variable Expansion Implementation of the Smith-Waterman Algorithm

被引：8

作者：

Hasan, Laiq ^{[1
]}

Al-Ars, Zaid ^{[1
]}

机构：

[1] Delft Univ Technol, Comp Engn Lab, NL-2628 CD Delft, Netherlands

来源：

2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20 | 2009年

关键词：

Bioinformatics; Sequence Alignment; Smith-Waterman Algorithm; FPGAs; Systolic Arrays; Recursive Variable Expansion;

D O I：

10.1109/IEMBS.2009.5332567

中图分类号：

R318 [生物医学工程];

学科分类号：

0831 ;

摘要：

In this paper, we present an efficient and high performance linear recursive variable expansion (RVE) implementation of the Smith-Waterman (S-W) algorithm and compare it with a traditional linear systolic array implementation. The results demonstrate that the linear RYE implementation performs up to 2.33 times better than the traditional linear systolic array implementation, at the cost of utilizing 2 times more resources.

引用

页码：3845 / 3848

页数：4

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