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Assessment of the parallelization approach of d2_cluster for high-performance sequence clustering

✍ Scribed by John E. Carpenter; Alan Christoffels; Yael Weinbach; Winston A. Hide

Publisher: John Wiley and Sons
Year: 2002
Tongue: English
Weight: 72 KB
Volume: 23
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.10025

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✦ Synopsis

Abstract

The exponential increase in expressed sequence tag (EST) sequence data amplifies the computational cost of clustering sequences such that new algorithms are required to analyze data at a greater rate. We have parallelized d2_cluster on a SGI Origin 2000 multiprocessor and observed a speedup of approximately 100× on 126 processors when processing a 15,876 EST dataset. The parallelized d2_cluster code is obtainable from the SANBI website (http://www.sanbi.ac.za/CODES). © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 755–757, 2002

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