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HIV sequence database

Variable Region Characteristics

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

Details: The tool accepts a set of aligned protein sequences in Fasta, IG, table, and other formats, along with an optional reference sequence.

Title of Analysis

Paste your alignment here

Use Sample Input

Clear Input Data
Or upload a data file
Prefix Summary
If your sequence names have information such as clade embedded as an alphanumeric prefix before a separator character (for example: A1_ or A1. or A1- or A1*) in the name, and you would like a summary by those values, click the check box.
Include a prefix summary
Select Positions
Use Alignment positions to
Use Reference positions to
Net Charge Options
You may choose how net charge is computed:
KRH = +, DE = -    (default)
KR = +, DE = -
Select Regions
If you input an HIV alignment that includes HXB2, check the regions you wish to have characterized.

Make sure you understand the explanation before using these options.
  V1:   Full loop (131-157)    Hypervariable region
  V2:   Full loop (158-196)    Hypervariable region
  V1+V2:   Full loop 131-157 + 158-196)    Hypervariable region
  V3:   Full loop (296-331)         (loop not hypervariable)
  V4:   Full loop (385-418)    Hypervariable region
  V5:   Full loop (460-469)    Hypervariable region
last modified: Wed Jul 13 08:24 2016

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