Zerg: a very fast BLAST parser library

被引：11

作者：

Paquola, ACM ^{[1
]}

Machado, AA ^{[1
]}

Reis, EM ^{[1
]}

da Silva, AM ^{[1
]}

Verjovski-Almeida, S ^{[1
]}

机构：

[1] Univ Sao Paulo, Inst Quim, Dept Bioquim, BR-05508900 Sao Paulo, Brazil

来源：

BIOINFORMATICS | 2003年 / 19卷 / 08期

基金：

巴西圣保罗研究基金会;

关键词：

D O I：

10.1093/bioinformatics/btg122

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Zerg is a library of sub-routines that parses the output from all NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx) and returns the attributes of a BLAST report to the user. It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers.

引用

页码：1035 / 1036

页数：2

共 4 条

[1] 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

[2] d2_cluster: A validated method for clustering EST and full-length cDNA sequences [J].

Burke, J ;

Davison, D ;

Hide, W .

GENOME RESEARCH, 1999, 9 (11) :1135-1142

[3] The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome [J].

Camargo, AA ;

Samaia, HPB ;

Dias-Neto, E ;

Simao, DF ;

Migotto, IA ;

Briones, MRS ;

Costa, FF ;

Nagai, MA ;

Verjovski-Almeida, S ;

Zago, MA ;

Andrade, LEC ;

Carrer, H ;

El-Dorry, HFA ;

Espreafico, EM ;

Habr-Gama, A ;

Giannella-Neto, D ;

Goldman, GH ;

Gruber, A ;

Hackel, C ;

Kimura, ET ;

Maciel, RMB ;

Marie, SKN ;

Martins, EAL ;

Nóbrega, MP ;

Paçó-Larson, ML ;

Pardini, MIMC ;

Pereira, GG ;

Pesquero, JB ;

Rodrigues, V ;

Rogatto, SR ;

da Silva, IDCG ;

Sogayar, MC ;

Sonati, MDF ;

Tajara, EH ;

Valentini, SR ;

Alberto, FL ;

Amaral, MEJ ;

Aneas, I ;

Arnaldi, LAT ;

de Assis, AM ;

Bengtson, MH ;

Bergamo, NA ;

Bombonato, V ;

de Camargo, MER ;

Canevari, RA ;

Carraro, DM ;

Cerutti, JM ;

Corrêa, MLC ;

Corrêa, RFR ;

Costa, MCR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (21) :12103-12108

[4] Multi-query sequence BLAST output examination with MuSeqBox [J].

Xing, LQ ;

Brendel, V .

BIOINFORMATICS, 2001, 17 (08) :744-745

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