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Whole Genome Comparison on a Network of Workstations

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5 Author(s)
Arpith Jacob ; Vellore Institute of Technology, India ; Sugata Sanyal ; Marcin Paprzycki ; Rajan Arora
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Whole genome comparison consists of comparing or aligning genome sequences with a goal of finding similarities between them. Previously we have shown how SIMD extensions used in Intel processors can be used to efficiently implement the, genome comparing, Smith-Waterman algorithm. Here we present distributed version of that algorithm. We show that on somewhat outdated hardware we can achieve speeds upwards of 8000 MCUPS; one of the fastest implementations of the Smith-Waterman algorithm.

Published in:

Parallel and Distributed Computing, 2007. ISPDC '07. Sixth International Symposium on

Date of Conference:

5-8 July 2007