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© Oxford University Press

Implementations of BLAST for Parallel Computer

Anne Juülich

The Gen ToolsTM Project The University of Texas System, Center for High Performance Computin Austin, Texas 78758-4497, USA

The BLAST sequence comparison programs have been ported to a variety of parallel computers – the shared memory machine Cray Y–MP 8/864 and the distributed memory architectures Intel iPSC/860 and nCUBE. Addi–tionally, the programs were ported to run on workstation clusters. We explain the parallelization techniques and consider the pros and cons of these methods. The BLAST programs are very well suited for parallelization for a moderate number of processors. We illustrate our results using the program blastp as an example. As input data for blastp, a 799 residue protein query sequence and the protein database PIR were used.

Received on September 4, 1993; accepted on August 1, 1994

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