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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.

Applications Note

Multiple sequence alignment in parallel on a workstation cluster

Justin Ebedes and Amitava Datta *

School of Computer Science and Software Engineering, University of Western Australia, Perth, WA 6009, Australia

Received on July 31, 2003; revised on November 10, 2003; accepted on December 24, 2003
Advance Access Publication February 5, 2004

Summary: Multiple sequence alignment is the NP-hard problem of aligning three or more DNA or amino acid sequences in an optimal way so as to match as many characters as possible from the set of sequences. The popular sequence alignment program ClustalW uses the classical method of approximating a sequence alignment, by first computing a distance matrix and then constructing a guide tree to show the evolutionary relationship of the sequences. We show that parallelizing the ClustalW algorithm can result in significant speedup. We used a cluster of workstations using C and message passing interface for our implementation. Experimental results show that speedup of over 5.5 on six processors is obtainable for most inputs.

Availability: The software is available upon request from the second author.

Contact: datta{at}csse.uwa.edu.au

* To whom correspondence should be addressed.


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