Customizing the Color Scheme of Nucleotide and Amino acid Sequences

Coloring schemes differ depending on the type of sequence, whether it's a nucletide or amino acid sequence. The Electropherogram and Quality color schemes are available only for nucleotide sequences while RasMol, Polarity, Hydrophobicity, Clustal and Structural AA color schemes are available only for protein sequences.

To change the color scheme, click Colors in the Sequence Viewer and select the color scheme you wish to use from the dropdown.

Color schemes 

By annotation color scheme

This colors the nucleotides and amino acids based on the annotation name. In the example below, when Color By annotation and Type FR is selected, nucleotides with the same annotation name and type will share an identical colour.

Electropherogram 

This colors nucleotides as follows:

Green: A
Blue: C
Black: G
Red:T

Quality 

This assigns a shade of blue to each nucleotide base based on its quality score. Dark blue for base quality Phred scores <20,>40. </20,>

Note that when the Quality color scheme is selected for sequences without quality score, the color scheme will default to the Geneious background color scheme.

RasMol 

This colors amino acids according to the Rasmol color scheme according to traditional amino acid properties. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition.

Bright red: D, Q
Blue: K, R
Mid blue: F, Y
Light grey: G
Dark grey: A
Pale blue: H
Yellow: C, M
Orange: S, T
Cyan: N, Q
Green: L, V, I
Pink: W
Flesh: P

Hydrophobicity 

This colors amino acids from red through to blue according to their hydrophobicity value,
where red is the most hydrophobic and blue is the most hydrophilic. The values of the color scale
are given in the figure below. These values are taken from Expasy

Polarity 

This colors amino acids according to their polarity as follows:

Yellow: Non-polar (G, A, V, L, I, F, W, M, P)
Green: Polar, uncharged (S, T, C, Y, N, Q)
Red: Polar, acidic (D, E)
Blue: Polar, basic (K, R, H)

Clustal 

This colors amino acids according to their properties and is adapted from Clustal to incude acidic residues as follows:

Orange: G, P, S, T 
Red: H, K, R 
Blue: F, W, Y 
Green: I, L, M, V 
Purple: D, E 

Structural AAs

This colors amino acids F, Y, W, P and G light green.