Question about multiple sequence alignment

[Robert C Oehmke]

Hi, 

 My name is Robert Oehmke and I'm a Computer Science PhD student at the
University of Michigan. The reason I'm emailing you is that I'm currently
fishing about for a dissertation topic and I did some previous work that
might be applicable to M.S.A, but I don't have the Biology background 
to see if it'd be useful. I was hoping that someone in this news group
could grant me some insight.

 The previous work I did was to use various methods, including a
large parallel computer to solve an instance of dynamic programming that
looks pretty similar to MSA. The size we solved it at looks to me to 
be (very) roughly equivalent to comparing 6 sequences of size n=200 using
what you term the rigorous method. I think my methods might be combinable
with the Carrillo & Lipman method to go even further. 

Now given the fact that my program takes around 6 hours to run on 
a parallel computer. Does it seems useful to be able to be able to compare
sequences exactly for this range of number of sequences and length of 
protein, or are the approximation methods good enough to render the extra 
work useless? Note, that the program is not fixed at a size of 6 and 200
the number of sequences could also be adjusted down to vastly increase the
length of the protein. 

Any help given be appreciated. 

Thank you for your time.

- Bob Oehmke