[BiO BB] protein clustering threshold

[Bossers, Alex]

Hhhhhhmmmm in addition: in prions a single polymorphism can determine
species specificity. Even within species a single poly can determine the
specificity of prion conversion reactions....
Just a thought, NOT to confuse........

Alex


> -----Oorspronkelijk bericht-----
> Van: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-
> admin at bioinformatics.org] Namens Hongyu Zhang
> Verzonden: woensdag 11 februari 2004 2:58
> Aan: bio_bulletin_board at bioinformatics.org
> Onderwerp: Re: [BiO BB] protein clustering threshold
> 
> 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.
> 
> --Hongyu
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