Question: Pfam Domain Annotation
8
gravatar for Cotsapas
9.9 years ago by
Cotsapas100
United States
Cotsapas100 wrote:

Greetings all - we have annotated a set of proteins with pfam domain calls. We would like a higher-level view of domain space (eg, dna-binding, catalytic, protein-binding, etc) rather than specific families. Anyone know of a family annotation table somewhere?

Chris

annotation sequence protein • 6.4k views
ADD COMMENTlink modified 9.9 years ago by User 616920 • written 9.9 years ago by Cotsapas100
8
gravatar for Khader Shameer
9.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

You can use Pfam2GO annotations http://www.geneontology.org/external2go/pfam2go

This is an automated mapping of GO terms to Pfam domains. Please note that Pfam2GO annotations may not be available for all the domains.

ADD COMMENTlink modified 9.9 years ago • written 9.9 years ago by Khader Shameer18k

additionally, I would suggest using Pfam clans of domains to get likely GO annotations for terms that don't have them

ADD REPLYlink written 9.9 years ago by Michael Kuhn5.0k

Michael, I agree that Clans can provide a global view of related protein domain families in Pfam. IMHO deriving GO annotation from the CLAN members will be tricky at times. Clan level relation may not be the be the best pool to derive functions for families with out Pfam2GO.

ADD REPLYlink written 9.9 years ago by Khader Shameer18k

Thanks Khader - we'll try it and see. C

ADD REPLYlink written 9.9 years ago by Cotsapas100
1
gravatar for User 6169
8.3 years ago by
User 616920
User 616920 wrote:

If it's a small set of proteins, you can use ProtoNet: http://www.protonet.cs.huji.ac.il/ There is a tool "Classify Your Protein". ProtoNet provides automatic hierarchical classification of proteins according to sequences.

ADD COMMENTlink written 8.3 years ago by User 616920
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