Zerg: A very fast BLAST parser library

Apuã C.M. Paquola; Abimael A. Machado; Eduardo M. Reis; Aline M. da Silva; Sergio Verjovski-Almeida

doi:10.1093/bioinformatics/btg122

Zerg: A very fast BLAST parser library

Apuã C.M. Paquola, Abimael A. Machado, Eduardo M. Reis, Aline M. da Silva, Sergio Verjovski-Almeida

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Summary: 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.

Original language	English (US)
Pages (from-to)	1035-1036
Number of pages	2
Journal	Bioinformatics
Volume	19
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btg122
State	Published - May 22 2003
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btg122

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title = "Zerg: A very fast BLAST parser library",

abstract = "Summary: 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.",

author = "Paquola, {Apu{\~a} C.M.} and Machado, {Abimael A.} and Reis, {Eduardo M.} and {da Silva}, {Aline M.} and Sergio Verjovski-Almeida",

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T2 - A very fast BLAST parser library

AU - Paquola, Apuã C.M.

AU - Machado, Abimael A.

AU - Reis, Eduardo M.

AU - da Silva, Aline M.

AU - Verjovski-Almeida, Sergio

N1 - Funding Information: Work supported by FAPESP, Fundac¸ão de Amparo a Pesquisa do Estado de São Paulo and CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil.

PY - 2003/5/22

Y1 - 2003/5/22

N2 - Summary: 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.

AB - Summary: 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.

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ER -

Zerg: A very fast BLAST parser library

Abstract

ASJC Scopus subject areas

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