HIV Sequence Database
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Programs and Tools
Search Interface retrieves HIV and SIV sequences, which can then be aligned and used to build trees Geography Search Interface retrieves HIV sequences based on geographical distribution Tools for working with sequences a complete list of our online tools, organized by function Alignments
HIV Premade Alignments includes Consensus and Ancestral Sequences, Subtype Reference Alignments (for use in trees, subtyping, and recombination analysis), and Complete Alignments (based on all sequences in the database) |
Information
HIV Sequence Compendia print or order a copy of our annual compendium and review articles Tutorials and other information unpublished web-based content posted on this site Links to other HIV/AIDS tools and information About this website
FAQ questions and answers that give general information about this website How to Cite this Database explains how to refer to this database in publications |
A link to jpHMM has been added to our Tools menu to make this subtyping/classification and recombination detection tool more accessible to the HIV community. This link currently goes to GOBICS (University of Goettingen) where it was developed together with the HIV Database team. A "local" version will be available soon. 22 March 2008
A beta version of a new tool, Protein Feature Accent, is now available. This user-friendly tool allows a user to highlight regions of interest on HIV protein structures. We will be adding features to this tool over the next few months, but the basics are in place. Suggestions for additional features are welcome. 21 March 2008
MOSAIC is a suite of related tools that can help in designing vaccine reagents, a web implementation of our vaccine design strategy for desiging full length mosaic proteins that give optimal potential epitope coverage.It assesses sequence diversity in terms of fragments of a specified length (e.g.9-mers, the length of a typical CTL epitope). Independent overall summaries of the number of perfect or close matches with the target sequence population can be obtained using Epicover, and levels of similarity spanning an alignment can be obtained with Posicover. 20 March 2008
The 14th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology will be held in Cape Town, South Africa, September 1-5, 2008. This workshop includes lectures and hands-on molecular bioinformatics training, in phylogenetic analyses and other types of genetic/protein sequence analysis. 19 March 2008
The 2006 HIV-1 web alignments are now available for download; the new HIV-2 and SIV alignments will follow shortly. We have also created a new download interface that gives access to all available alignments (web, subtype reference, and consensus/ancestral). This interface allows you to clip out a slice from the alignments if you provide the reference sequence coordinates. 25 February 2008
