HIV molecular immunology database


Epitope Density Plots


These plots show the number of reported human HIV-1 epitopes spanning each amino acid, for all HIV-1 proteins in the database. The positions are based on the standard HXB2 reference strain numbering. Our database is a summary of all HIV-1 epitopes reported in the literature, so these plots reflect the sampling biases of the field. This is particularly problematic as some HIV-1 proteins are studied much more intensely than others in natural infection, and some proteins are used more often as a vaccine, with responses mapped. Within a given protein, however, sampling is more consistent across the length of the protein, so regions of very high epitope density relative to low density in a single protein (like within Gag) are more likely reflect something inherent in the immunogenicity of the local region.

The antibody maps essentially reflect a summary of known linear epitopes. There is a PDF version of each plot available for download.

There are separate pages showing the distribution of CTL/CD8+, T-Helper/CD4+, and Antibody epitopes for each protein. These pages also have links to the data files to reproduce these plots.

Human Epitope Density Plot

PDF version: count_by_aa.pdf

Detailed plots for each protein

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