Consensus from Multiple Alignments

[Andrea Hansen]

Tim Spahlinger <txs at po.cwru.edu> writes:
Hi Tim,
what about GENEDOC? A nice free tool for multiple alignments. 

GeneDoc - A Full Featured Multiple Sequence Alignment Editor, 
Analyser and Shading Utility for Windows. 
     http://www.psc.edu/biomed/genedoc/ 

Another way is to look at the long list of online tools :
http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/
Online_Multiple_Alignment/

Andrea

> 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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