[Protein-analysis] Re: Newbie question about microarray analysis

Rex Eastbourne rex.eastbourne at gmail.com
Tue May 30 21:00:35 EST 2006

Thanks a lot Austin!

Austin P. So (Hae-Jin) wrote:
> Rex Eastbourne wrote:
> > I just have a plain list of 200 proteins, without data from the
> > experiment. I need to cluster the proteins by their inherent
> > characteristics (function, ancestry). I used the protein database on
> > the NCBI website to get the sequences. Now, I want to take all these
> > 200 sequences and get some measure of how similar each is to each
> > other. I figure this would require some specific software that would
> > allow me to enter all the proteins and see how they're related. I found
> > ProtoNet, but it seems you can only enter one protein and explore its
> > specific cluster. Are there any other tools for this I might not be
> > aware of?
> Oh...then just ignore everything I've said...you seem to be asking a
> number of different unrelated questions though...
> This is not an easy project to do for you then, if you are going to go
> outside of the standard tools at NCBI.
> A simple comparison can be made through the BLAST server:
> http://www.ncbi.nlm.nih.gov/BLAST/
> A good resource for constructing phylogenic trees (which is what you
> seem to want to do here):
> http://evolution.genetics.washington.edu/phylip/software.html
> Good luck
> austin

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