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  1. Jalview
  2. JAL-3046

Ignore gapped positions in conservation calculation

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.12.0
    • Component/s: analysis, gui
    • Labels:
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      Description

      A user preference and interactive setting to change whether gaps are counted in the Physicochemical property calculation.

      Current defaults are hardcoded: conservation is only reported for columns containing 25% or less gaps, and the gap character is treated like any other amino acid symbol (i.e. it has 'all properties') if it is more than 3% abundant.

      Ideally, one should be able:
      1. Ignore gapped sites in the property calculation.
      2. Ignore %age gaps when deciding whether to report conservation, or adjust that threshold.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: