![]() ![]() 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. Should the image not be broken, the analysis can continue and this specific item can be ignored in future tests.N-linked glycosylation is a posttranslational modification that has significantly contributed to the rapid evolution of HIV-1. This way, the Website Analyzer gives a warning to indicate that the image needs to be analysed manually. This can be identified in the Analyzer under "Error Log" (error message: URL excluded by Robots.txt). Why does the Qualidator Website Analyzer show a warning for a broken image, which in reality is not displayed? This is possible if the Qualidator Website Analyzer has been excluded by Robots.txt and therefore cannot analyse the image. User Agent can be adapted in the licensed versions only. Are the Robots.txt rules observed? Yes, incl. ![]() Why are some tests disabled? Registered users can select more tests than anonymous users depending on the licence, customers are able to activate all tests. Free registration doubles the amount of pages and allows you perform more detailed analysis. Why does the test run stop after x amount of pages? Should you not have registered under ,Options', you can do so and enable an additional amount of pages. ![]() Warnings arise from the HTML validation, hints from the Qualidator tests. What is the difference between a warning and a hint? A warning refers to syntax and a hint to style. ![]()
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