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HIV sequence database



AnalyzeAlign

Purpose: Show weblogos, calculate frequency by position, and find variants in an alignment. Explanation.

Input
Alignment
[Sample Input]
Paste or upload alignment icon
  
  
Use LANL database alignment icon
    Alignment
type
Filtered web  Web  Subtype reference  Compendium 
    Organism HIV-1/SIVcpz  HIV-2/SIVsmm   Other SIV
    Region
    Subtypes All   Major subtypes (A B C D F G CRF01 CRF02)
Sequence type nucleotide   amino acid
Positions/range to analyze icon
Total positions ≤ 200!
Range numbers refer to icon alignment columns, including gaps residues of 1st sequence residues of HXB2 (K03455)
Group the sequences icon Report results for all sequences as a single group
Report separate results for subsets of sequences (email results)
      Group sequences by:
   the characters in field of names delimited by
first character(s) in names
paste or upload grouped sequence names (example)
    
    
I am using a LANL alignment; group sequences by subtypes (the first field)
      Combine logos into a page:  
       Concatenate as a x matrix  
   Orientation: Portrait   Landscape  
   Include removed logos:  
Email results
plus Logo options
minus Other options


Related links:

last modified: Fri May 13 14:35 2016


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