<i>MPBLAST</i> : improved BLAST performance with multiplexed queries

BioinformaticsPublished 1 November 2000Open access

Ian Korf, Warren Gish

DOI10.1093/bioinformatics/16.11.1052

Source URL

Citations24

SJR quartileQ1

SJR score2.45

SNIP1.47

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TL;DR

A program, MPBLAST, is developed that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed.

Abstract

UNLABELLED: 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

Keywords

Computer ScienceBiochemistry, Genetics and Molecular Biology

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