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Last update on 25. Nov 2018 .
ARB: a Short Introduction
ARB_EDIT4 - Sequence primary and secondary structure editor
Sequence color mapping
ARB_EDIT4/Properties/Sequence color mapping
The ARB_EDIT4 editor uses two tables to translate the original sequence into a colored displayed sequence:
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'
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
You may use this feature to show:
A simplified version of your amino acid alignment.
Only YR instead of ACGTU
Only ambiguous symbols
No bugs known