A parallel Smith-Waterman algorithm based on divide and conquer

被引：0

作者：

Zhang, F ^{[1
]}

Qiao, XZ ^{[1
]}

Liu, ZY ^{[1
]}

机构：

[1] Chinese Acad Sci, Comp Technol Inst, Beijing 100080, Peoples R China

来源：

FIFTH INTERNATIONAL CONFERENCE ON ALGORITHMS AND ARCHITECTURES FOR PARALLEL PROCESSING, PROCEEDINGS | 2002年

关键词：

biological sequence alignment; dynamic programming; divide and conquer; parallel;

D O I：

暂无

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Biological sequence comparison is an important tool for researchers in molecular biology. There are several algorithms for sequence comparison. The Smith-Waterman algorithm, based on dynamic programming, is one of the most fundamental algorithms in bioinformatics. However the existing parallel Smith-Waterman algorithm needs large memory space. As the data of biological sequences expand rapidly, the memory requirement of the existing parallel Smith-Waterman algorithm has becoming a critical problem. For resolving this problem, we develop a new parallel Smith-Waterman algorithm using the method of divide and conquer, named PSW-DC Memory space required in the new parallel algorithm is reduced significantly in comparison with existing ones. A key technique, named The C&E method, is developed for the implementation of the new parallel Smith-Waterman algorithm.

引用

页码：162 / 169

页数：8

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