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


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.


BACKGROUND
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).
De Oliveira
T
T
Molecular Virology and Bioinformatics, Africa Centre/University of Natal, Durban, South Africa. toliveira@mrc.ac.za
Miller
R
R
Tarin
M
M
Cassol
S
S
D003628:Database Management Systems; D030541:Databases, Genetic; D005827:Genetics, Microbial / Q000379:methods*; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface