WebPSSM (position-specific scoring matrices ) is a bioinformatic tool for predicting HIV-1 coreceptor usage from amino acid or nucleotide sequences of the third variable loop (V3) of the envelope gene. When a nucleotide sequence is entered, it will be translated to amino acid sequence first. If a nucleotide sequence contains ambiguous bases, it will be translated to all possible amino acid sequences.
Mullins Molecular Retrovirology Lab, University of Washington.
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Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.
Jensen MA, Li FS, van ‘t Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI.
J Virol. 2003 Dec;77(24):13376-88.