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Last update on 25. Nov 2018 .
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    Sequence color mapping

    OCCURRENCE

    ARB_EDIT4/Properties/Sequence color mapping

     

    DESCRIPTION

    The ARB_EDIT4 editor uses two tables to translate the original sequence into a colored displayed sequence:

    First Step:

    Each character in each sequence is translated into a new character and a color index (0..9) using the definitions from the 'Sequence color mapping' subwindow.
    • There are different sets (1..8) of color shemes, using two columns for each set.
    • At the top of the window you may choose which set is used for translation of nucleotides and aminoacids.
    • The first column shows the characters which should be translated/replaced.
    • The Nth + 1 column holds the translation instruction for set N. Each of its fields has two characters:
      • the character which should replace the original value, or '=' if no translation should be performed.
      • a color index for this character, between 0 and 9.

      The default for the translation instruction is '=0'

    Second Step:

    Each of the color indices (0..9) corresponds to one of the colors defined in <Properties/Change colors & fonts>, namely to
    index     corresponding color
    0         SEQUENCES
    1         HELIX(1)
    2         COLOR 2
    3         COLOR 3
    .         .
    .         .
    9         COLOR 9
     

    EXAMPLES

    You may use this feature to show:

    • A simplified version of your amino acid alignment.
    • Only YR instead of ACGTU
    • Only ambiguous symbols
    • etc.

     

    BUGS

    No bugs known