coloured sequence-editor (Protein !) ?

Luc Simon lsimon at alnus.for.ulaval.ca
Tue May 4 09:31:42 EST 1993


In article <1993May3.175609.16 at immunbio.mpg.de>, HAESS at IMMUNBIO.MPG.DE
(Gunther H) wrote:
> 
>[stuff deleted...] 
> 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     

Why not simply designing a few colored fonts for the mac, where some
letters are assigned background color. Each one could have a name
informative about the coloring scheme: "AA Hydrophobicity" or "AA size" and
the like. Then, using one's favorite editor, you simply select the portion
of sequence to be color-coded and apply the desired font....et voila!

Such a thing as already been done: the font BKGCuclc is the best example (I
don't know where it comes from!!) and is VERY useful to view DNA
alignements, for example in the PAUP editor.


Luc Simon
CRBF, Universite Laval
Quebec
lsimon at alnus.for.ulaval.ca




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