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Tweaking PrettyBox

Michael Coyne mjcoyne at warren.med.harvard.edu
Tue May 14 09:45:48 EST 1996

Hi all...

PrettyBox seems to shade similar residues only if those resides are in a
coloumn that contributes to the consensus.  If no consensus is called, no
shading occurs, even if the coloumn is composed of similar residues.  For
example, consider the following alignment of residues, analyzed with
/THR=1.0, /PLU=3.0, and /PAIR=1.5, 1.0, 0.5:

L (black)
L (black)
F (dark)
L (black)
V (pale)
. (white - a gap)

L (black, called consensus)

This is as expected, as F is similar to L (matrix score 1.2, thus similar
(dark)), and V is somewhat similar to L (matrix score 0.8, thus pale).  No
problem.  But, consider the following alignment:



Nothing is called here (understandable), but shouldn't these residues be
shaded to indicate though no one species predominates, they are all
similar to one another (I-L matrix score 0.8, I-V 1.1, L-L & V-V 1.5).  I
have been unable to hit upon a combination of THReshold, PLUarilty and
PAIR that will shade these (or any similar residues) in the absence of a
called consensus.

Anybody have any information or ideas?

Thanks -

Mike Coyne

 //=\   Michael J. Coyne                           phone: (617) 432-2675
 \=//   Channing Laboratory, Room 318              FAX:   (617) 731-1541
  //=\  180 Longwood Avenue
  \=//  Boston, MA 02115           email: mjcoyne at warren.med.harvard.edu
   //=\                                   mcoyne at argo.net

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