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coloured sequence-editor (Protein !) ?

Dr. R.J. Beynon beynonrj at liverpool.ac.uk
Thu Apr 29 07:37:10 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

Well, here's suggestion 1, to get things rolling...

R,K (H?)       : red  (+ive)
D,E            : blue (-ive)
N,Q            : magenta (cf blue)
C,M            : yellow (sulphur, or sulfur :-) )
A,I,L,M,W,F,V  : black ('oily')
S,T,Y,G        : white (not 'oily')

This is only partial colour coding, of course. One could use shades
to indicate 'flavour' and 'size' - making D light red, and E dark red
for example. but even that gets complex with the hydrophobics.  

As with most schemes, it's the simple ones that work, and get remembered.

I might also ask for one option - to use, say, orange if the C is in a
disulphide bond, as opposed to being free C.

Opinions, alternatives anyone?

Rob Beynon, Proteolysis Group, Liverpool, UK

p.s. then we can have 'protease red' and 'protease blue' etc :-)

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