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
LRFC at ICR
Chester Beatty Laboratories
London
Leanne at icr.ac.uk
