MPBLAST: Improved BLAST performance with multiplexed queries

Ian F Korf, W. Gish

Research output: Contribution to journalArticle

19 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1052-1053
Number of pages2
JournalBioinformatics
Volume16
Issue number11
StatePublished - 2000
Externally publishedYes

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ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

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