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.

Detalhes bibliográficos

Principais autores:	Osório,E.C., Souza,J.E. de, Zaiats,A.C., Oliveira,P.S.L. de, Souza,S.J. de
Formato:	Digital revista
Idioma:	English
Publicado em:	Associação Brasileira de Divulgação Científica 2003
Acesso em linha:	http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007
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