Mathog, David R. (2003) Parallel BLAST on split databases. Bioinformatics, 19 (14). pp. 1865-1866. ISSN 1367-4803. http://resolver.caltech.edu/CaltechAUTHORS:20111020-082203402
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BLAST programs often run on large SMP machines where multiple threads can work simultaneously and there is enough memory to cache the databases between program runs. A group of programs is described which allows comparable performance to be achieved with a Beowulf configuration in which no node has enough memory to cache a database but the cluster as an aggregate does. To achieve this result, databases are split into equal sized pieces and stored locally on each node. Each query is run on all nodes in parallel and the resultant BLAST output files from all nodes merged to yield the final output.
|Additional Information:||© 2003 Oxford University Press. Received on July 10, 2002; revised on February 20, 2003; accepted on April 18, 2003. I thank Caltech and the Howard Hughes Medical Institute for support. I also thank R. Andrew Cameron, Erich Schwarz and Leonard Thomas, for their comments on the manuscript.|
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|Deposited By:||Tony Diaz|
|Deposited On:||24 Oct 2011 22:26|
|Last Modified:||24 Oct 2011 22:26|
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