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Hypermut

Analysis & Detection of APOBEC-induced Hypermutation

Purpose: To document the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence. See details below. For a simple "quick and dirty" scan for hypermutants, try the QC Tool.

Input
Indicate sequence format of input
  Note: Sequences must be aligned, in-frame if possible, and of equal length.
Paste alignment here
[Sample Input]
Or upload alignment file
Restrict analysis to subregion of alignment from bp to bp (optional)
Hypermut 2.0 Customized Options
These options apply only to Hypermut 2.0 analysis, and have no effect on the Original Hypermut output. For typical analyses of APOBEC-induced hypermutation in HIV, these options should be left in their default settings.
     
  Mutation    
   Upstream 
context: 

 
 Downstream
 context:
Enforce
context:
Customize Hypermut pattern:

On reference sequence
On both sequences
On query sequence
     
Customize control pattern:

Output
Analyses to perform: Both   Original Hypermut   Hypermut 2.0     

Details: The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. Please choose the reference sequence carefully. For example, for an intrapatient set, the reference should probably be the most common form in the first sampled time point; for a set of unrelated sequences, the reference should probably be the consensus sequence for the appropriate subtype. Before using, please read:

References:

last modified: Tue Aug 14 10:04 2012


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

 
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