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Implementation Issues of Optimized Buffer Management for BLAST

Melissa LemosJosé Antônio Fernandes de MacedoLuiz SeibelFabio PortoRogério CostaRoberto CavalcanteVitor Medina Cruz

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.

http://www.lbd.dcc.ufmg.br:8080/colecoes/e-science/2010/67753_1.pdf

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