![]() In the N-linked Glycosylation Site Comparison program (N-Glyco Site Compare), input sequences are automatically aligned with the HIV-1 reference strain HXB2 (accession number: K03455. Visualization methods are available for all results (see details in ‘Server Output’ section below). The web server interface is implemented through HTML and Bootstrap JavaScript. Implementation of both features has been written in Java. Second, the server optimizes HIV-1 sequence alignment by using the N-linked glycosylation site as alignment anchor. ![]() First, through an automated pipeline, changes at N-linked glycosylation sites within each variable loop region, as well as loop lengths, can be easily tracked and compared between populations of HIV sequences. Two key features distinguish our HIV-1 N-linked Glycosylation Site Analyzer from other HIV-1 sequence analysis tools and servers. As a result, our N-linked Glycosylation Site Analyzer serves as a valuable gateway for exploring HIV-1 diversity in immunologically important genomic regions, contributing to an improved understanding of host–virus interaction and enhanced viral vaccine strain selection. Furthermore, considering the functional importance and conserved patterns of N-linked glycosylation sites, we have implemented in this server a feature that optimizes HIV-1 sequence alignment using N-linked glycosylation sites in variable loops as alignment anchors. This server provides an automated platform for mapping and comparing N-linked glycosylation sites within variable loops between populations of HIV-1 sequences. To address the importance of N-linked glycosylation sites in HIV-1 and problems in analyzing variable loops as described above, we present development of the HIV N-linked Glycosylation Site Analyzer, available at. As a result, variable loops are typically excluded from phylogenetic analyses ( 6, 7, 10), leading to frequent underestimation of HIV-1 diversity in immunologically important genomic regions. Of note, although immunologically and evolutionarily important, HIV-1 variable loops are notoriously known as difficult to analyze owing to extraordinary viral diversity in these regions ( 11). Both changes are important measurements of HIV-1 diversity ( 10). Changes of N-linked glycosylation sites within variable loops, as well as changes of lengths of variable loops imposed by frequent indels (insertion and deletions), are highly favored in HIV-1 ( 1, 9). In HIV-1, N-linked glycosylation sites are enriched within the variable loops, which contain multiple neutralizing antibody-binding sites ( 9). Evaluation of co-receptor usage has demonstrated a tendency for higher mutation rates, higher net positive charges and fewer glycosylation sites within HIV-1 strains with CXCR4 co-receptor usage ( 8). reported an increase in N-linked glycosylated sites during late stages of HIV-1 infection ( 7). Changes in N-linked glycosylation sites have also been linked to both disease stage and co-receptor usage. Comparison between neutralization-sensitive and neutralization-resistant HIV-1 strains shows a higher number of glycosylation sites associated with the resistant clusters ( 6). Changes in N-linked glycosylation sites in HIV-1 can induce conformational changes in Envelope gp120, diminishing binding of many gp120-specific antibodies ( 5). Highly glycosylated regions are referred to as immunologically silent faces ( 4), reducing antigenicity and restricting access to chemokine receptors. A typical N-linked glycosylation site requires the context of the amino acid pattern N-X- ( 2), with X being any amino acid except Proline ( 3). Strategic placement and loss and gain of N-linked glycosylation sites are one of the most important evolutionary mechanisms adopted by HIV-1 to generate its extraordinary sequence diversity ( 1). The HIV N-linked Glycosylation Site Analyzer web server is available at. Availability of this web server solves one of the difficult problems in HIV gp120 alignment and analysis imposed by the extraordinary HIV-1 diversity. ![]() Furthermore, this server allows for refinement of HIV-1 sequence alignment by using N-linked glycosylation sites in variable loops as alignment anchors. This server provides an automated platform for mapping and comparing variable loop N-linked glycosylation sites across populations of HIV-1 sequences. The web server described here, the HIV N-linked Glycosylation Site Analyzer, was developed to facilitate study of HIV diversity by tracking gp120 N-linked glycosylation sites. In particular, enrichment of N-linked glycosylation sites can be found within Envelope variable loops, regions that play an essential role in HIV pathogenesis and immunogenicity. ![]() N-linked glycosylation is a posttranslational modification that has significantly contributed to the rapid evolution of HIV-1. ![]()
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