displaying alignments (thanks)

Michael D. Baron "/G=michael/S=baron/OU=morbillivirus/OU=pirbright/OU=i a h/" at AFRC.ac.uk
Tue Jan 4 07:14:55 EST 1994

Dear netters,

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 me.
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)

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