2003 International Conference on Parallel Processing (ICPP'03) Space and Time Optimal Parallel Sequence Alignments Kaohsiung, Taiwan October 06-October 09 ISBN: 0-7695-2017-0
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 (\frac{{m + n}} {p}) space but supboptimal O (\frac{{(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 (\frac{{mn}} {p}) time but O (m + \frac{n} {p}) space. We close this gap by presenting an algorithm that achieves both time and space optimality, i.e. requires only O (\frac{{m + n}} {p}) space and O (\frac{{mn}} {p}) time. We also present an experimental evaluation of the proposed algorithm on an IBM xSeries cluster.
Citation:
Stjepan Rajko, Srinivas Aluru, "Space and Time Optimal Parallel Sequence Alignments," icpp, pp.39, 2003 International Conference on Parallel Processing (ICPP'03), 2003 Usage of this product signifies your acceptance of the Terms of Use. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||