displaying alignments

Peter Rice rice at embl-heidelberg.de
Wed Dec 22 03:43:35 EST 1993

In article <2f6vhj$8uk at mserv1.dl.ac.uk>, "Michael D. Baron"
<"/G=michael/S=baron/OU=morbillivirus/OU=pirbright/OU=i a h/"@AFRC.ac.uk>
> I am looking for a program which will allow me to display/print the 
> alignment I have made of a set of protein sequences. Ideally, it will 
> shade, or otherwise highlight, the residues that match a consensus, 
> allowing for conservative replacements; it would be nice to 
> distinguish highly conserved from less conserved residues.
> I have tried PrettyPlot which works, but does not allow one to 
> distinguish between degrees of conservation (residues are either in 
> the box or out), and the PrettyPrint option in Don Gilbert's wonderful 
> SeqApp, which only highlights identical residues.

As I did PRETTYPLOT I suppose I should join this thread too. The calculation
of the consensus in PRETTYPLOT started out as a copy of GCG's PRETTY program,
but I soon found a few changes were needed - especially for low pluralities
where there could be a choice of equally valid residues. Like Rick
Westerman's PRETTYBOX this is not strictly a GCG program, but an
extension to the package. As GCG distributes it in their unsupported
division I have got quite used to seeing it cited as "GCG" (and, after all,
they did write the code that remains from PRETTY). Also like PRETTYBOX
it suffers from confusion caused by the difference between the threshold
score of 1.0 for the consensus and the value of 1.5 for identical residues
in GCG's usual comparison matrix.

It is not possible to satisfy everyone with these programs. For example,
should the consensus be calculated (as with PRETTY, PRETTYBOX and
PRETTYPLOT), should it be provided by the user (and if so, how), should
the user be able to edit the plot after it has been generated (we have
some users who really enjoy editing PostScript output, but maybe an
intermediate format could be created that allowed easy changes to be
made :-)

If you feel brave, you could try modifying the source code of PRETTYPLOT
(send any suggestions to me please), or PRETTYBOX (ditto to Rick Westerman)
to suit your own preferences. I let several users here loose on PRETTYPLOT
and got some good suggestions back that way.

 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice at EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       69012 Heidelberg
 Fax:     +49-6221-387306                     |       Germany

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