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Bioinformatics Vol. 19 no. 8 2003
Pages 1035-1036
© 2003 Oxford University Press

Applications Note

Zerg: a very fast BLAST parser library

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

Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo 05508-900, São Paulo, SP, Brazil

Received on September 11, 2002 ; revised on December 3, 2002 ; accepted on January 16, 2003

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.

Availability: http://bioinfo.iq.usp.br/zerg

Contact: verjo{at}iq.usp.br

* To whom correspondence should be addressed.


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