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coloured sequence-editor (Protein !)?

Fri Apr 30 15:26:00 EST 1993

Don Gilbert (gilbertd at sunflower.bio.indiana.edu) wrote:
>: If someone will suggest what colors should be associated with
>: what amino acids for an editor display I will put it into
>: a coming release of seqapp.  At some point I'll make it
>: user-definable, but give me a starting selection.

>: -- 
>: Don Gilbert                                     gilbert at bio.indiana.edu
>: biocomputing office, biology dept., indiana univ., bloomington, in 47405

Can I contribute with a few comments and suggestions:

One program already exists which enables you to display a multiple
alignement of proteins with specific colours corresponding to specific
aa. It is called SOCOL (Attwood and Parry-Smith 1991) and works on a 
multiple alignement generated by clustal (Higgins and Sharp) and modified 
by somap. I don't have the reference nor the adresses of the authors, though.
It allows you to make a choice on which property you want to show ie
residue type, positional variability index, structure prediction index, as
far as I understood it well. We only use residue type colouring here. 
The simple colour code used is the following:
basic = blue
acidic = red
LAVIM = gray
GP = braun
STNQ = green
FYW = purple
C = yellow
gap = white

Using more colours, I'd like to propose the following suggestions/modifs:

R = turquoise (basic)
K = blue (basic, "hydrophobic")
H = violet (aromatic, slightly basic)
Y, W = magenta (aromatic, polar)
F = dark braun (aromatic)
I, L = light braun (hydrophobic, aliphatic)
V, A = gray (hydrophobic, aliphatic, small)
M = olive (hydrophobic, sulphur, start)
C = yellow (S-S, small, hydrophobic)
G = sand/ochre (tiny)
S, T = orange (small polar)
N, Q = pink (polar)
E, D = red (acidic)
P = green (small, coil)
and I think also as important to add
stop =  white letter on dark background
unknown,X, gap = dark letter on white background

This follow some sort of logic with mixing of colours when common properties
are shared. ie turquoise -> blue -> violet -> magenta
or magenta -> red -> pink -> orange. It is also intuitive (dark colours = 
aromatic, hydrophobic; bright colours = polar; light = small)
It is based on a panel of 
complementary colours (red, magenta, violet, blue, turquoise, green, olive,
yellow, ochre/sand, orange, pink, red...) + braun, gray, white and black.

Any comments? 

Eric Schoonejans
John Innes Institute
Colney Lane
NR4 7UH Norwich UK

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