[BiO BB] help with bacterial protein sequence comparisons

Ketil Malde ketil.malde at imr.no
Tue May 15 03:10:56 EDT 2012

Phoebe Rice <price at uchicago.edu> writes:

> Blast gives me pages of 99% identical proteins (mostly from other
> S. aureus strains), and I'm too lazy to pick "representatives"
> manually from further down the list.  What is the best way to get a
> list of related proteins that are all, say, <90% identical to other
> proteins in the list? 

I don't know if these are in UniProt, but if they are, you can search
the UniRef 90 (or 50) database, which consists of proteins with at most
90 (50) percent similarity.

If I haven't seen further, it is by standing in the footprints of giants

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