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Bioinformatics Vol. 19 no. 1 2003
Pages 153-154
© 2003 Oxford University Press

Applications Note

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences

T. De Oliveira 1,*, R. Miller 2, M. Tarin 1 and S. Cassol 1

1 Molecular Virology and Bioinformatics, Africa Centre/University of Natal, Durban, South Africa
2 Inpharmatica, Ltd., London, UK

Received on February 26, 2002 ; revised on June 5, 2002 and July 9, 2002 ; accepted on July 24, 2002

Motivation: Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting.

Design and Results: GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases.

Availability: GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net)

Contact: toliveira{at}mrc.ac.za

* To whom correspondence should be addressed.


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