Multiple sequence alignment in parallel on a workstation cluster

Amitava Datta, J. Ebedes

    Research output: Contribution to journalArticle

    33 Citations (Scopus)

    Abstract

    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.
    Original languageEnglish
    Pages (from-to)1193-1195
    JournalBioinformatics
    Volume20
    Issue number7
    DOIs
    Publication statusPublished - 2004

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