with reference to my posting to the net just before Christmas, I would
like to thank all those of you who took the time and trouble to reply.
I must especially thank (and apologise to) Rick Westerman: now that
he has explained what PRETTYBOX is doing, it is clear that it does
what he intended it to do, and I am properly corrected. I would like
to emphasise that I did not really mean to say that all the programs
were "wrong" (that they didn't do what I want is in no way the same as
saying that "they all have faults" - maybe what I want to do is something
stupid ;-) ). Since different scientists are
going to want to emphasise different things with their data, naturally
programs will differ in what they are designed to do. I was merely
making a general enquiry in the hope that someone had had the same aim
As it happens, a number of people communicated that they *had* wanted
to do what I described, but none of the programs available did it
(because, of course, they were designed to do something else). As Mark
Reboul suggested, it might be worth a little discussion about what
kind of rules we want an alignment *display* program to follow when it
makes a decision as to what residues to highlight. For example, I
think of such a highlighting tool as something to automate the
questions that I would ask about each position in the alignment if I
was doing the whole thing manually, or if I was inspecting a new
alignment, and I start the process by asking
"What is the consensus residue?"
"Is there a consensus?".
The second level is then something like
"Is this a fully conserved (all/mostly identical) or partially
conserved (all/mostly similar) residue?"
(Note that I am avoiding specifiying how such questions are answered by
a program, or how concepts like 'similar' are defined.)
If we could reach a consensus (;-)) on what us users wanted, perhaps
this would be of use to someone who is (going to be) writing software.
What do other sequence-gazers think?
Michael Baron (BARON at AVRI.AFRC.AC.UK)