Consensus from Multiple Alignments
webmaster at bioinformatik.de
Wed Oct 25 13:42:35 EST 2000
Tim Spahlinger <txs at po.cwru.edu> writes:
what about GENEDOC? A nice free tool for multiple alignments.
GeneDoc - A Full Featured Multiple Sequence Alignment Editor,
Analyser and Shading Utility for Windows.
Another way is to look at the long list of online tools :
> I'm either very naive in making a request for such a dynamic
> program, or I'm too new and inexperienced with such things
> 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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