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Bioinformatics Advance Access published online on April 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti424
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 19, 2004
Revised March 17, 2005
Accepted March 31, 2005

Article

EGene: a configurable pipeline generation system for automated sequence analysis

Alan M. Durham 1*, André Y. Kashiwabara 1, Fernando T. G. Matsunaga 2, Paulo H. Ahagon 2, Flávia Rainone 1, Leonardo Varuzza 2, and Arthur Gruber 2

1 Depto. de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo SP, 05508-900, Brazil
2 Depto. de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo SP, 05508-900, Brazil

* To whom correspondence should be addressed.
Alan M. Durham, E-mail: alan{at}ime.usp.br


  Abstract

Summary: EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required. EGene comes with CoEd, a visual tool to facilitate pipeline construction and documentation. A series of components to build pipelines for sequence processing is provided.

Availability: http://www.lbm.fmvz.usp.br/egene/.

Supplementary information: http://www.lbm.fmvz.usp.br/egene/.


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