Mapping of positive selection sites in the HIV genome in the context of RNA and protein structural constraints

Background The HIV-1 genome is subject to great variability. On the one hand, there are recognized pressures that target the virus and resulting in escape and adaptation. On the other hand, there is a requirement for sequence conservation because of functional and structural constraints. Mapping the sites of positive selective pressure on the viral genome generates a reference for understanding the limits to viral escape, and can serve as a template for the discovery of sites of genetic conflict with known or unknown host proteins.