pp-Blast: a "pseudo-parallel" Blast

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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Main Authors: Osório,E.C., Souza,J.E. de, Zaiats,A.C., Oliveira,P.S.L. de, Souza,S.J. de
Format: Digital revista
Language:English
Published: Associação Brasileira de Divulgação Científica 2003
Online Access:http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007
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spelling oai:scielo:S0100-879X20030004000072003-04-08pp-Blast: a "pseudo-parallel" BlastOsório,E.C.Souza,J.E. deZaiats,A.C.Oliveira,P.S.L. deSouza,S.J. de Blast Search engines Fasta 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.info:eu-repo/semantics/openAccessAssociação Brasileira de Divulgação CientíficaBrazilian Journal of Medical and Biological Research v.36 n.4 20032003-04-01info:eu-repo/semantics/othertext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007en10.1590/S0100-879X2003000400007
institution SCIELO
collection OJS
country Brasil
countrycode BR
component Revista
access En linea
databasecode rev-scielo-br
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region America del Sur
libraryname SciELO
language English
format Digital
author Osório,E.C.
Souza,J.E. de
Zaiats,A.C.
Oliveira,P.S.L. de
Souza,S.J. de
spellingShingle Osório,E.C.
Souza,J.E. de
Zaiats,A.C.
Oliveira,P.S.L. de
Souza,S.J. de
pp-Blast: a "pseudo-parallel" Blast
author_facet Osório,E.C.
Souza,J.E. de
Zaiats,A.C.
Oliveira,P.S.L. de
Souza,S.J. de
author_sort Osório,E.C.
title pp-Blast: a "pseudo-parallel" Blast
title_short pp-Blast: a "pseudo-parallel" Blast
title_full pp-Blast: a "pseudo-parallel" Blast
title_fullStr pp-Blast: a "pseudo-parallel" Blast
title_full_unstemmed pp-Blast: a "pseudo-parallel" Blast
title_sort pp-blast: a "pseudo-parallel" blast
description 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.
publisher Associação Brasileira de Divulgação Científica
publishDate 2003
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007
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AT souzajede ppblastapseudoparallelblast
AT zaiatsac ppblastapseudoparallelblast
AT oliveirapslde ppblastapseudoparallelblast
AT souzasjde ppblastapseudoparallelblast
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