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PubMed · 12700823

pp-Blast: a "pseudo-parallel" Blast.

E C Osório·J E de Souza·A C Zaiats·P S L de Oliveira·S J de Souza
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Abstract

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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Computing MethodologiesCost-Benefit AnalysisDatabase Management SystemsGenome, HumanHumansInternetTime FactorsUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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E C Osório, J E de Souza, A C Zaiats, P S L de Oliveira, S J de Souza. 2003-04-08. pp-Blast: a "pseudo-parallel" Blast.. https://doi.org/10.1590/s0100-879x2003000400007

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