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L.M. Wiedemann mblmw at s-crim1.dl.ac.uk
Wed Jul 31 11:14:23 EST 1996

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
Leanne at icr.ac.uk

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