Symbol comparisons in PRETTY

Victor Jongeneel vjongene at eliot.unil.ch
Mon Jul 10 09:03:41 EST 1995

Hello all!

I was trying to get PRETTY (GCG) to do a relatively simple thing, viz., 
printing an alignment from a .MSF file with a consensus at the bottom, and 
each sequence in the alignment with '-' at positions where it matches the 
consensus, or the amino acid code at positions where it doesn't.  This is in 
principle possible using the /CON and /DIF='-' command-line switches.

The output however is not quite what you would expect.  It seems that the 
consensus is calculated using a very permissive comparison table, and that 
only one member of the permitted values in the consensus is displayed.  For 
example, at one position PRETTY decided that W and R both matched the 
consensus, which was given as W, while the sequences containing R did just get 
a '-' to indicate a match.  This of course is unacceptable.

So the question(s): Is it the PrettyPep.Cmp file that does this?  Is there a 
relatively easy way to change this behavior?  Why was this default matrix 
chosen in the first place? (I can't think of a single good reason myself).

I'll post an example if the description above turns out to be insufficient.  
Thanks to all for feedback/help.

Victor J.

|C. Victor Jongeneel, PhD, Associate Member     |
|Ludwig Institute for Cancer Research           |
|CH-1066 EPALINGES      Switzerland             |
|Tel: +41-21-692-5994   FAX: +41-21-653-4474    |
|E-mail: CornelisVictor.Jongeneel at isrec.unil.ch |

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