Andy Phillips andy.phillips at bbsrc.ac.uk
Thu Aug 1 04:39:25 EST 1996

L.M. Wiedemann wrote:
> HELP.  I am trying to get a nice alignment for a publication.  This
> looked like the ticket.  I have spent two days now and keep getting
> output that isn't exactly what I want.  If I just put my sequences in
> with equal weighting and accept the defaults, the insert in the last
> sequence (the only one with a 20 aa insert or so) comes up black.  So
> I tried changing the THR parameter, PLU parameter, weighting etc and
> can get the insert not to come up, but now the entire first sequence
> comes up black, even if no match is below.  I don't want a printed
> consensus below.  I just want to emphasize the similarities between
> the top sequence and those below it.  Best of all, would be to show
> everytime one of the sequences below match the top sequence, even
> ignoring the fact that the other 3 of 4 sequences match each other.
> That might be a tall order.  I would be happy if neither the top or the
> bottom sequences were boxed when they didn't really match anything.
> If anyone out there has experience with this, I would be eternally
> grateful.  I have read all the documentation I could find, but nothing
> really helped.
> Leanne Wiedemann
> Chester Beatty Laboratories
> London
> Leanne at icr.ac.uk

I've struggled to get prettybox to produce exactly what I want on many occasions. You 
could try another program to produce the shading - Genedoc is free (on 
http://www.cris.com/~ketchup/genedoc.shtml) and does a reasonable job. There's 
also Boxshade. However, if you can't get any program to do exactly what you want, it is 
possible to edit the postscript output produced by prettybox - for example, I wrote a 
simple routine to produce couloured output instead of B&W. You can also add boxes, 
arrows etc with a little knowledge of the PS programming language. It's very easy to 
change shading of individual residues: open up the PS output file in a text 
editor, there will be some garbage at the beginning, then the sequences will be listed, 
one residue at a time, block by block.


(I) 8   77.0 black
(I) 8   76.0 black
(V) 8   75.0 light
(I) 8   74.0 black
(W) 9   77.0 black
(W) 9   76.0 black
(W) 9   75.0 black
(W) 9   74.0 black

is the first two columns of a lineup: the character in brackets is the amino acid, the 
first number is the X coordinate, the second number is the Y coordinate and the last 
item is the shading colour. So the sample above generates:


with all residues shaded black (white on black) except the V. To unshade a residue, 
simply change 'black' to 'white' (the other options are dark, light and pale). The 
difficult part is finding the characters you want to change in a big lineup, as the 
residues are listed by column in separate blocks.

There are also lots of other useful commands that can change the aspect of the output 
file (e.g. '1.0 0.9 scale' at the start of the sequence listing will shrink the output 
by 10% in the Y-dimension - useful for fitting a lineupinto a paper!

Remember to save the file in ASCII format if you use a wordprocessor - better to use a 
text editor such as PFedit. Then just copy the file to a PS printer.

Hope this helps,


 Email  : andy.phillips at bbsrc.ac.uk  : University of Bristol
 Home   : andy at cycad.demon.co.uk     : IACR Long Ashton Research Station 
 Phone  : +44-1275-549257            : Long Ashton
 Fax    : +44-1275-394281            : Bristol, BS18 9AF, UK
 WWW    : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html

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