HIV N-linked Glycosylation Site Analyzer



Introduction


This site is devoted for analyzing the N-linked glycosylation sites in HIV-1.

  • N-linked glycosylation is a post-translational modification that has significantly contributed to the rapid evolution of HIV-1. In particular, enrichment of N-linked glycosylation sites can be found within variable loops in the HIV gp120 Envelope, regions that play an essential role in HIV pathogenesis and immunogenicity. The loss and gain of N-linked glycosylation sites is one of the most important evolutionary mechanisms adopted by HIV-1. Here is the reference in case you want to know more about the N-linked glycosylation sites in HIV-1.


Features


This site provides two features for analyzing HIV-1 N-glycosylation sites.

  1. N-glycosylation Site Compare: provides an automated platform for mapping and comparing N-linked glycosylation sites within variable loops between populations of HIV-1 sequences. The comparison groups can be sequences under different conditions. For instance, sequences sampled at different time points, of different subtypes, and associated with different risk factors. Here is an example of such an analysis.

    Run N-Glyco Site Compare »


  2. V Loop Alignment: To address the functional importance and conserved patterns of N-linked glycosylation sites, this program optimizes HIV-1 sequence alignment using N-linked glycosylation sites in variable loops as alignment anchors. The optimized alignment solves one prominent problem in HIV-1 alignment in which the variable loops are notoriously known as difficult to analyze due to extraordinary viral diversity in these regions (See the reference).

    Run V Loop Alignment »



References


  • Timothy Shaw, Ming Zhang. HIV N-linked Glycosylation Site Analyzer and Its Futher Usage in Anchored Alignment. Nucleic Acids Res. 2013 Jun 8.