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...
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Associação Brasileira de Divulgação Científica
2003-04-01
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doaj-fc222ef0528f4efdbea6e724158362802020-11-25T02:42:23ZengAssociação Brasileira de Divulgação CientíficaBrazilian Journal of Medical and Biological Research0100-879X1414-431X2003-04-0136446346410.1590/S0100-879X2003000400007pp-Blast: a "pseudo-parallel" BlastE.C. OsórioJ.E. de SouzaA.C. ZaiatsP.S.L. de OliveiraS.J. de SouzaWe 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.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007BlastSearch enginesFasta |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
E.C. Osório J.E. de Souza A.C. Zaiats P.S.L. de Oliveira S.J. de Souza |
spellingShingle |
E.C. Osório J.E. de Souza A.C. Zaiats P.S.L. de Oliveira S.J. de Souza pp-Blast: a "pseudo-parallel" Blast Brazilian Journal of Medical and Biological Research Blast Search engines Fasta |
author_facet |
E.C. Osório J.E. de Souza A.C. Zaiats P.S.L. de Oliveira S.J. de Souza |
author_sort |
E.C. Osório |
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 |
publisher |
Associação Brasileira de Divulgação Científica |
series |
Brazilian Journal of Medical and Biological Research |
issn |
0100-879X 1414-431X |
publishDate |
2003-04-01 |
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. |
topic |
Blast Search engines Fasta |
url |
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003000400007 |
work_keys_str_mv |
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1724774308158373888 |