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pfam hierarchy?

Nicola Mulder mulder at
Wed Jul 24 02:15:48 PDT 2002

Hi Lisa
I work on the InterPro project which is an integration of the major
protein signature databases into a single resource. It includes Pfam,
ProDom, Prints, Prosite, TIGRFAMs and SMART, all of whch use different
methods to diagnose protein families or domains. Pfam itself does not
have a hierarchy since no 2 Pfam HMMs should ever overlap on a sequence,
however there may be a Prints or other signature which defines a
subset/subfamily of a Pfam family. In InterPro we found many such cases
so we have a hierarchy of parent/child relationships. We also have a
contains/found in relationship which is used when a domain is found in a
family of proteins. In this way there is some sort of hierarchy of Pfam
in relation to other signature database signatures. For more information
Where possible InterPro entries are also mapped to GO terms. Let me know
if you want any more particular information.
Nicky (InterPro)

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