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pfam hierarchy?

Nicola Mulder mulder at ebi.ac.uk
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
see: http://www.ebi.ac.uk/interpro
Where possible InterPro entries are also mapped to GO terms. Let me know
if you want any more particular information.
Regards
Nicky (InterPro)


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