pp-Blast: a "pseudo-parallel" Blast

• Main Authors: E.C. Osório, J.E. de Souza, A.C. Zaiats, P.S.L. de Oliveira, S.J. de Souza
• Format: Article
• Language: English
• Published: Associação Brasileira de Divulgação Científica 2003-04-01
• Series: Brazilian Journal of Medical and Biological Research
• Subjects: Blast; Search engines; Fasta
• Online Access: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007

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.