Massive Multiple Sequence Alignment tools?

Brian Foley brianf at med.uvm.edu
Tue May 7 18:32:51 EST 1996

	I have found the answer to my problem and although
it is not simple, it is potentially very powerful.  I have
not run the analysis yet, so I can't provide too many details yet
but hopefully I can follow up in a couple of weeks with more
information.  If anyone else is interested, feel free to
e-mail me directly.
	The solution is to use Hidden Markov Methods
such as SAM http://www.cse.ucsc.edu/research/compbio/sam.html
and HMMER http://genome.wustl.edu/eddy/hmm.html
to generate a "model" which is somewhat like a "consensus
sequence" but retains information about the percent of
sequences which contain a particular base (or amino acid)
at each site.  THe model is a full matrix of data about
an alignment, rather than just a single consensus sequence.
The "model" can then be used to query the database, and
I have been told that I should be able to adjust that 
query to give me out put that contains the information 
needed to automate a full multiple sequence alignment of all
the sequences in the database that match my model to some
cut-off value I specify.
	I'll let you know how it works.

*  Brian Foley               *  btf at t10.lanl.gov                   *
*  T-10, MS-K710, LANL       *  http://hiv-web.lanl.gov            *
*  Los Alamos, NM 87545 USA  *  http://www.uvm.edu/~bfoley         *

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