By Topic

Space and time optimal parallel sequence alignments

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

2 Author(s)
S. Rajko ; Dept. of Comput. Sci., Iowa State Univ., Ames, IA, USA ; S. Aluru

We present the first space and time optimal parallel algorithm for the pairwise sequence alignment problem, a fundamental problem in computational biology. This problem can be solved sequentially in O(mn) time and O(m+n) space, where m and n are the lengths of the sequences to be aligned. The fastest known parallel space-optimal algorithm for pairwise sequence alignment takes optimal O(m+n/p) space but suboptimal O((m+n)2/p) time, where p is the number of processors. On the other hand, the most space economical time-optimal parallel algorithm takes O(mn/p) time but O(m+n/p) space. We close this gap by presenting an algorithm that achieves both time and space optimality, i.e. requires only O(m+n/p) space and O(mn/p) time. We also present an experimental evaluation of the proposed algorithm on an IBMxSeries cluster

Published in:

Parallel Processing, 2003. Proceedings. 2003 International Conference on

Date of Conference:

9-9 Oct. 2003