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Minerva Biotecnologica 2003 September;15(3):191-3

language: English

DNCBLAST: a par­allel ­BLAST for com­put­er clus­ters

Rossi I., Marchignoli D., Fariselli P., Beltrami R., Medini D., Casadio R.

CIRB Biocomputing Unit and Laboratory of Biophysics, Department of Biology, University of Bologna, Bologna, Italy


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The ­BLAST ­suite is ­designed to effi­cient­ly per­form­ing ­sequence sim­i­lar­ity search­es in bio­log­i­cal data­bas­es, and in ­this ­task it is con­sid­er­ably fast­er ­than oth­er heur­is­tic algo­rithms. However, espe­cial­ly for ­large ­genomes, ­BLAST per­for­manc­es can be optim­ised. We ­describe a sim­ple and effec­tive way to intro­duce par­allel­ism in the ­BLAST ­code by apply­ing a “­divide and con­quer” (DNC) ­approach ­based on split­ting and dis­trib­ut­ing the orig­i­nal data­base. In ­this way ­DNCBLAST can effi­cient­ly run on com­put­er clus­ters and over­comes the mem­o­ry lim­i­ta­tion of a sin­gle ­machine.

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