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Variable Region Characteristics

Purpose: Variable Region Characteristics analyzes protein sequences for V1, V2, V3, V4, V5 lengths, glycosolations, 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 (131-157)    Hypervariable region (132-152)
  V2:   Full loop (158-196)    Hypervariable region (185-190)
  V1+V2:   Full loop (131-157 + 158-196)    Hypervariable region (132-152 + 185-190)
  V3:   Full loop (296-331)         (loop not hypervariable)
  V4:   Full loop (385-418)    Hypervariable region (396-410)
  V5:   Full loop (460-469)    Hypervariable region (460-465)
Use alignment positions to
Use reference positions to
Prefix summary icon Include
Title of Analysis icon
Feature Data (optional)
Feature data icon
Delimiter Space   Comma   Tab  
Mismatched names icon Ignore mismatched sequence names between alignment and feature data
Binarize values icon Not needed; values are 1, 0, or -1
Values are continuous; set values ≥ median to 1, and values < median to 0
Header icon The first row of feature data is a header
last modified: Thu Mar 8 12:37 2018


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

 
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