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HIV sequence database



Variable Region Characteristics

Purpose: Variable Region Characteristics analyzes protein sequences for V1, V2, V3, V4, V5 lengths, glycosylations, and net charge. For details, see the explanation.

Input
Paste alignment icon

[Sample Input]
Or upload a file
Options
Net charge icon KRH = +, DE = -       KR = +, DE = -
Specify regions icon Select HIV-1 variable regions (for HIV-1 ENV alignment that includes HXB2)
V1: Full loop (130-158)*    Hypervariable region (132-152)
V2: Full loop (157-197)*    Hypervariable region (185-190)
V1+V2: Full loop (130-157 + 158-197)*    Hypervariable region (132-152 + 185-190)
V3: Full loop (295-332)*         (loop not hypervariable)
V4: Full loop (385-418)    Hypervariable region (396-410)
V5: Full loop (459-470)*    Hypervariable region (460-465)
* Results for V1, V2, V3, and V5 include one position immediately before and another immediately after the region so that glycosylation sites at the boundaries are counted.
Use alignment positions to
Use reference positions to
Group summary icon Include summary by grouped sequences according to
    first character(s) in sequence names
the column in field of sequence names delimited by
paste or upload grouped sequence names (see example below)

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last modified: Fri Aug 5 14:38 2022


Questions or comments? Contact us at seq-info@lanl.gov.

 
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