1. UGENE
  2. UGENE-6548

Add "Weak similarities" color scheme to the Alignment Editor


    • Type: New Feature New Feature
    • Status: Open Open
    • Priority: Critical Critical
    • Resolution: Unresolved
    • Affects Version/s: 1.32
    • Fix Version/s: None
    • Component/s: Basic-MSA
    • Labels:
    • Affect Type:


      Add a new color scheme "Weak similarities" to the color schemes in the Alignment Editor ("Color" combo box on the "Highlighting" tab on the options panel, "Colors" menu in the "Actions" main menu and the Alignment Editor context menu).


      The color scheme should be available for alignments of the following alphabets:

      • Standard DNA
      • Standard RNA
      • Extended DNA
      • Extended RNA

      Characters priority

      When there is a choice between two characters and and it is not specified by other rules which character to color, follow priorities: T>U>G>C>A>B>D>H>K>M>R>S>V>W>Y>N.

      Coloring rules

      1. Do not color gaps ("-"), i.e. use black font and white background.
      2. Residues should be colored according to their percentage number in the column (use the priorities, described above, in case of equal percentage numbers):
        • Residues with the most frequency/priority in the column:
          • background color: light blue (#00FFFF)
          • font color: blue (#0000FF)
        • Residues with the 2nd frequency/priority:
          • background color: white (#FFFFFF)
          • font color: crimson (#FF00FF)
        • Residues with the 3rd frequency/priority:
          • background color: white (#FFFFFF)
          • font color: black (#000000)
        • Residues with the 4th frequency/priority:
          • background color: gray (#C0C0C0)
          • font color: black (#000000)
        • Other residues:
          • background color: white (#FFFFFF)
          • font color: orange (#FF6600)

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            • Assignee:
              Olga Golosova
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