MPBLAST:: improved BLAST performance with multiplexed queries

被引：17

作者：

Korf, I ^{[1
]}

Gish, W

机构：

[1] Washington Univ, Sch Med, Genome Sequencing Ctr, St Louis, MO 63108 USA

[2] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63108 USA

来源：

BIOINFORMATICS | 2000年 / 16卷 / 11期

关键词：

D O I：

10.1093/bioinformatics/16.11.1052

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1052 / 1053

页数：2

共 7 条

[1]

Altschul SF, 1996, METHOD ENZYMOL, V266, P460

[2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[3]

ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999

[4] IDENTIFICATION OF PROTEIN CODING REGIONS BY DATABASE SIMILARITY SEARCH [J].

GISH, W ;

STATES, DJ .

NATURE GENETICS, 1993, 3 (03) :266-272

[5]

GISH W, 1996, WU BLAST 2 0

[6] METHODS FOR ASSESSING THE STATISTICAL SIGNIFICANCE OF MOLECULAR SEQUENCE FEATURES BY USING GENERAL SCORING SCHEMES [J].

KARLIN, S ;

ALTSCHUL, SF .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1990, 87 (06) :2264-2268

[7] APPLICATIONS AND STATISTICS FOR MULTIPLE HIGH-SCORING SEGMENTS IN MOLECULAR SEQUENCES [J].

KARLIN, S ;

ALTSCHUL, SF .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (12) :5873-5877

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