Africa Centre bioinformatics unit
This capacity building project aims to resuscitate the bioinformatics unit based at the Africa Centre laboratories in Durban. The Africa Centre bioinformatics unit will contain bioinformatics servers and applications need for the generation and analysis of sequences produced at the ABI 3100 sequencer machine at the AC laboratory. At the moment, two Mac based computers have been ordered and will contain most of the bioinformatics applications used on HIV sequence analysis. A backup system is also been planned to secure the raw sequence data produced at the laboratory. A number of internal capacity building workshops are planned to 2010. The objective of these workshops is to equip researchers at the AC lab with basic knowledge on HIV sequence editing and bioinformatics skills needed to analyze data produced in the others AC sequencing projects.
Southern African Treatment and Resistance Network (SATuRN) database (SATuRN-DB)
This project objective is to implement and maintain a Southern African collaborative HIV drug resistance database. The database used is the RegaDB, an open source clinical and research drug resistance database, which has been implemented at our bioinformatics server hosted at the MRC http://bioafrica.mrc.ac.za The database is currently been populated with clinical and genotypic data from ARV treatment programs in Southern Africa. The database contains published and unpublished data produced at collaborative research institutes (including the AC, National Institute of Communicable Diseases, University of Pretoria, University of the Free State and Stellenbosh University).
The database development and support is provided by a team formed by the project investigator (Dr. Tulio de Oliveira), the original developers of RegaDB (Dr. Koen Deforche and Pieter Libin) in Belgium, two data enterers (two positions based at the Africa Centre) and a system administrator at the MRC. The team is working together with collaborators to annotate and analyse a growing body of genotypic data (at present 1,246 sequences are stored in the database) from treatment programmes in Southern Africa. The data stored at SATuRN-DB is available to partners in a password protected web-interface at the bioafrica.net website.
HIV bioinformatics tools currently in development at bioafrica.net
1) HIV-1 Phylotyping Tool –
Web-address: http://atgc.lirmm.fr/phylotype/
The HIV-1 phylotyping tool is produced in collaboration with Prof. Olivier Gascuel research group at LIRMM/CNRS, Montpellier Univ. II. This tool was developed with the objective to analyse large sequence (genotype) datasets using a phylogenetic framework. The tool allows the identification of “phylotypes” which are clusters in phylogenetic trees associated with external annotations such as resistance mutations or geographic origin. The HIV-1 phylotyping tool was constructed with the vision to analyze datasets to be produced by the combination of genotypes with surveillance and treatment data stored at ACIDS and ARTEMIS databases at the Africa Centre. The submission of the first publication of the HIV-1 Phylotyping Tool is schedule to 2010. The tool will be applied to local research as soon as large sequences projects (please see list of grants submitted) are produced at the AC laboratory.
2) Surveillance of Viral Resistance Tool –
Web-address: http://bioafrica.mrc.ac.za/micropop/
The Surveillance of Viral Resistance Tool is a bioinformatics tool aimed at the analysis of high-throughput genotypic data of HIV-1, Hepatitis B and C virus (HBV and HCV). This tool is developed in collaboration with Dr. Robert Gifford (Oxford and Aaron Diamond AIDS Research Center) and Dr. Robert Shafer (Stanford Univ.). This tool allows large amount of viral surveillance data to be analyzed for drug resistance mutations in a few minutes. The tool interface also allows different rounds of genotypic data produced in surveillance studies to be compared. This tool is filling a gap in the current viral bioinformatics field by providing a fast and reliable tool for the analysis of expanding sequence datasets such as the ones stored at SATuRN-DB in South Africa and the UK Drug Resistance Database.
3) REGA HIV-1 Subtyping tool -
Web-address: http://www.bioafrica.net/rega-genotype/html/subtypinghiv.html
The REGA HIV-1 Subtyping tool is one of the most widely used HIV bioinformatics tools worldwide (over 350,000 HIV sequences submitted and approximately 100 citations since original publication in 2005). The tool is an automated method for HIV-1 subtyping and recombination analysis. Currently developments include re-coding the program using a more robust JAVA framework, updating reference databases, and coding new classification rules for the detection of HIV-1 recombination. The user interface has also been updated to allow submission of large datasets (up to 1,000 sequence per session). The new version (version 3) is under final testing stage and it will be submitted for publication soon.