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