| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary
- ARB_EDIT4 - Sequence primary and secondary structure editor

Related topics:

# Sequence color mapping

- OCCURRENCE
- DESCRIPTION
- EXAMPLES
- BUGS

## 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