Implementation Issues of Optimized Buffer Management for BLAST

  • Melissa Lemos PUC-Rio
  • José Antônio Fernandes de Macedo UFC
  • Luiz Seibel PUC-Rio
  • Fabio Porto LNCC
  • Rogério Costa PUC-Rio
  • Roberto Cavalcante PUC-Rio
  • Vitor Medina Cruz PUC-Rio

Abstract


Comparing sequences is one of the basic operations every Life Science scientist must execute. The most popular sequence comparison algorithm is BLAST. This paper presents experimental results of a buffer management strategy that optimizes the simultaneous execution of a set P of BLAST processes. The essence of the strategy is to cycle all the sequences in the database through a buffer so that all BLAST processes will perform their comparison synchronously.

References

Altschul, S.F.,et al (1990), A Basic Local Alignment Search Tool. Journal of Molecular Biology, 215, 403-410.

Lemos, M., Lifschitz, S. (2003), Memory Management for BLAST Processing, 1st International Workshop on Biological Data Management in Database and Expert Systems Applications (DEXA), Prague, Czech Republic, (2003) 5-9.
Published
2010-07-20
How to Cite

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LEMOS, Melissa; MACEDO, José Antônio Fernandes de; SEIBEL, Luiz; PORTO, Fabio; COSTA, Rogério; CAVALCANTE, Roberto; CRUZ, Vitor Medina. Implementation Issues of Optimized Buffer Management for BLAST. In: BRAZILIAN E-SCIENCE WORKSHOP (BRESCI), 4. , 2010, Belo Horizonte/MG. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2010 . p. 217-220. ISSN 2763-8774.