MPBLAST: Improved BLAST performance with multiplexed queries

Ian F Korf, W. Gish

Research output: Contribution to journalArticle

19 Citations (Scopus)

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

Fingerprint

Throughput
Databases
Query
Multiplexing
Sequencing
Batch
Speedup
Proportion

ASJC Scopus subject areas

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

Cite this

MPBLAST : Improved BLAST performance with multiplexed queries. / Korf, Ian F; Gish, W.

In: Bioinformatics, Vol. 16, No. 11, 2000, p. 1052-1053.

Research output: Contribution to journalArticle

Korf, Ian F ; Gish, W. / MPBLAST : Improved BLAST performance with multiplexed queries. In: Bioinformatics. 2000 ; Vol. 16, No. 11. pp. 1052-1053.
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