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Bioinformatics Vol. 16 no. 11 2000
Pages 1052-1053
© 2000 Oxford University Press

Applications Note

MPBLAST : improved BLAST performance with multiplexed queries

Ian Korf 1 and Warren Gish 1

1 Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, S. Louis, MO 63108, USA

Received on June 8, 2000 ; revised on August 10, 2000 ; accepted on August 11, 2000

Summary: We have developed a program, MPBLAST, that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed. Throughput was observed to increase in reciprocal proportion to the component sequence length. For sequencing read-sized queries of 500 bp, an order of magnitude speed-up was seen.

Availability: Free (see http://blast.wustl.edu)

Contact: {ikorf, gish}@watson.wustl.edu


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