[BiO BB] protein clustering threshold

Hongyu Zhang forward at hongyu.org
Tue Feb 10 20:58:20 EST 2004

I also remember hearing from somewhere that a single mutation at active sites
can change the activity of a protein from catalyzing one reaction to another.
I need to find the the exact example. Can anyone help me, please? I don't think
Prion is a good example, because my question is not about whether one protein
can have multiple functions.

Dan, thanks for the Uniprot example, but I found that some of the pair-wise
percentages of identities within the cluster are far less than 90% (e.g.,
between representative P51857 and member P52895 is 57.3% based on CLUSTALW). I
think it was caused by the clustering algorithm used in the data set. Another
problem in the UniRef90 XML file is that it doesn't come with Evidence code,
which makes it hard to tell whether the annotations are from experimental
results or electronic annotations. The latest TrEMBL provides this evidence
code, which I am going to give a try. I will keep you guys posted. BTW, I also
have a Perl XML parser, which is based on the XML::Twig module, but I am not
familiar with the automatic conversion between XML schema and SQL tables.

Thanks again.


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