pp-Blast: a "pseudo-parallel" Blast.
We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.
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Instituto Ludwig de Pesquisa sobre o Câncer, São Paulo, SP, Brasil. sandro@compbio.ludwig.org.br
de Souza
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JE
Zaiats
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de Oliveira
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PS
de Souza
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SJ
D003205:Computing Methodologies; D003362:Cost-Benefit Analysis; D003628:Database Management Systems / Q000191:economics; D015894:Genome, Human; D006801:Humans; D020407:Internet; D013997:Time Factors; D014584:User-Computer Interface