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:
A good resource for constructing phylogenic trees (which is what you
seem to want to do here):