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Space and time optimal parallel sequence alignments

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

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