Bioinformatics tools for HIV

Allows to identify strains of HIV with BLAST.
Directly callable from our HIV sequencing software GensearchHIV.

WebPSSM is a bioinformatic tool for predicting HIV-1 coreceptor usage from the amino acid sequence of the third variable loop (V3) of the envelope gene. Directly callable from our HIV sequencing software GensearchHIV.

This tool is designed to use phylogenetic methods in order to identify the subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods.

On submitting a sequence containing the V3 region of the HIV-1 envelope protein gp120 below, you will obtain a sequence alignment to the consensus sequence given in Pfeifer and Lengauer and a prediction whether the corresponding virus is capable of using CXCR4 as a coreceptor (R5/X4 or X4 variants) or not (R5 variants).