Consensus from Multiple Alignments

Tim Spahlinger txs at po.cwru.edu
Wed Oct 25 10:53:27 EST 2000


THANK YOU VERY MUCH!!!!

GENEDOC appears to be just what I need!!!

Andrea Hansen wrote:
> 
> 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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