Paper Info
Title
Parallelization of a local similarity algorithm.
Abstract
The local similarity problem is to determine the similar regions within two given sequences. We recently developed a dynamic programming algorithm for the local similarity problem that requires only space proportional to the sum of the two sequence lengths, whereas earlier methods use space proportional to the product of the lengths. In this paper, we describe how to parallelize the new algorithm and present results of experimental studies on an Intel hypercube. The parallel method provides rapid, high-resolution alignments for users of our software toolkit for pairwise sequence comparison, as illustrated here by a comparison of the chloroplast genomes of tobacco and liverwort.
Year
DOI
Venue
1992
10.1093/bioinformatics/8.2.155
COMPUTER APPLICATIONS IN THE BIOSCIENCES
Field
DocType
Volume
Sequence alignment,Pairwise comparison,Dynamic programming,Computer science,Parallel algorithm,Parallel computing,Algorithm,Software,Computer program,Bioinformatics,Hypercube,Intel iPSC
Journal
8
Issue
ISSN
Citations 
2
0266-7061
11
PageRank 
References 
Authors
3.34
6
4
Name
Order
Citations
PageRank
Xiaoqiu Huang138358.13
W Miller21301295.71
Scott Schwartz315553.87
R C Hardison418239.09