Consensus from Multiple Alignments

Tim Spahlinger txs at po.cwru.edu
Wed Oct 25 08:16:12 EST 2000


Hi,

I'm either very naive in making a request for such a dynamic
program, or I'm too new and inexperienced with such things
but:

Can somebody recommend a web site (preferred) or a software
package (I'd rather save my limited funding) that will give
me a consensus sequence of bases derived from the multiple
alignments of several sequences?  For example:

	temp1  AATGCCGA
	temp2  AATGGCGA
	temp3  AATGCCGA

    consensus  AATGCCGA

I've used ClustalW which indicates conservation at base
positions.  But, I have ALOT of sequences to align and if
even 1 base out of 100 within a column is different the "*"
of a conserved column will be missing, forcing me to look
for where the substitutions are and to count how many
substitutions are made.  I really need a consensus sequence.

ClustalX will graphically show where substitutions are made
but doesn't offer a consensus (at least I haven't figured
out how to get one from the graphic display; trying to print
the graphic display is another mystery to me)!

THANKS in advance for your help!!!!!






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