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  1. Jalview
  2. JAL-891

Adapt the existing sequence logo to visualize base-pair interactions

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.7_gsoc11, 2.8
    • Fix Version/s: 2.7_gsoc11
    • Component/s: gui
    • Labels:
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      Description


      The existing 'consensus' sequence logo is calculated using 'per column' symbol frequencies. This idea can be extended to pairwise sequence logos, where for an alignment like:
      >sa
      CCCGU
      >sb
      UUUGC

      and secondary structure:
      ((.))

      The logo at each position reflects the percentage of each type of base pair:

      Position 1: [ CU ] 50%; [UC] 50%.
      Position 2: [ UG ] 50%; [ CG ] 50%.

      Position 4 and 5 would give the inverse view, ie:

      Position 1: [ UC ] 50%; [ CU ] 50%.
      Position 2: [ GU ] 50%; [ GC ] 50%.

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            Assignee:
            jprocter James Procter
            Reporter:
            janengelhardt Jan Engelhardt
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              Dates

              Created:
              Updated: