14th International AIDS Conference Barcelona, Spain - July 7-12, 2002

Int Conf AIDS 2002 Jul 7-12; 14:(abstract no. A10030)

de Oliveira TP, Miller R, Cassol S
Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, UND, Durban, South Africa

BACKGROUND: Evolutionary analysis of viral and bacterial genomes requires multiple bioinformatics tools and specialized sequence datasets. Installing and learning software packages, locating and compiling large public databases is time-consuming and difficult.

OBJECTIVE: To develop an integrated Linux-based interface that lessens the complexities of input/output file formatting between modules and provides microbiologists/virologists with the high-throughput expertise needed to analyse and annotate their own sequences.

METHODS: Genetic Data Environment (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 (HIV-1, HCV, HTLV, HPV, HHV-8), bacterial (TB) and parasitic (malaria, trypanosomiasis) genomes. Each microbial interface is designed for local access and contains the entire Genbank sequence set, BLAST-formatted databases and datasets for phylogenetic analysis. GDE for Linux and its microbial menus can be freely downloaded (http://www. bioafrica.net). Results/

CONCLUSIONS: A fast and complete interface that performs sophisticated bioinformatics and evolutionary analyses, and which can be easily adapted to other microbial pathogens and installed on fast computer clusters, or even on laptops. Future Directions: Continue development of microbe-specific menus for a wide range of pathogens. A demonstration will be presented at the 8th European Workshop of Virus Molecular Evolution and the UNDP/WHO Tropical Diseases Bioinformatics Workshop. Course attendees will be invited to participate in the construction of new menus in their field of interest.

020707
A10030

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