coloured sequence-editor (Protein !) ?

Gunther H HAESS at IMMUNBIO.MPG.DE
Mon May 3 11:56:09 EST 1993


In <francis.736118661 at monod> francis at monod.Biol.McGill.CA writes:

> beynonrj at liverpool.ac.uk (Dr. R.J. Beynon) writes:
> 
> >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')
> 
> >Opinions, alternatives anyone?
> 
> 
> What is the proposed background colour for these different "greys"
> (oily and not oily)?
> 
> f.
> 
> 
> --
> | B.F. Francis Ouellette     * francis at monod.biol.mcgill.ca *
> |
> |      "Je cherche a` comprendre"  Jacques Monod



I wrote a little file-viewer for the VAX, that's able to display 
aa's in different, user-defined colours. Because the VAX doesen't support
colours in  textmode, I performed a REGIS(Graphics)-output. So its 
disadvantages are, that it's working very slowly and it's not an editor.

But the groups of aa with the same colours by default in this Program are

K R H                 kations         black on red
E D                   anions          black on blue
S T Q N               polar           black on yellow
V L I A W F C M Y     not polar       black on green
P G                   "special"       black on white
  
I think it's better to use a coloured background instead of coloured letters,
because if you want to read the letters, it's better they're in one color.
And if you want to distinguish different groups of aa's, it's better to have
more coloured area than only the letters themselves.


Instead of programming a whole editor for the MAC, I think it would be a good
idea of using a kind of macro with a present word-processor. Does anybody know 
about such a macro-tool for "WORD for MAC" ?


Gunther Haess, 
MPI-IB Freiburg/Germany
haess at immunbio.mpg.de     




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