Variability Analysis of HIV-1 gp120 V3 Region: IV. Distribution Functions for Intra- and Inter- Subtype Amino Acid Hamming Distances

• Published in: Journal of biomolecular structure & dynamics Vol. 15; no. 5; pp. 877 - 885
• Main Authors: Shchelkanov, Michael Yu, Starikov, Nicole S., Yaroslavtsev, Ilya V., Tsvetkov, Philip O., Yudin, Alex N., Denisov, Maxim V., Slavsky, Alexander A., Vedenov, Alexander A., Karamov, Edward V.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis Group 01-04-1998
• Subjects: AIDS/HIV; Amino Acids; HIV Envelope Protein gp120 - chemistry; Humans; Mathematical Computing; Peptide Fragments - chemistry
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.1998.10508209

Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures (see ref. 17) for HIV-I V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.