Find all domains in a list of proteins
I would like to get a list of all domains of all proteins in my list.
Browsing STRING, I noticed from the the domain structures (displays images from SMART database) that there are a lot of GEF-domians, but I cannot batch extract or batch search. I found no batch search on SMART or PFAM.
I could not find an easy tool. To find this in uniprot, or pfam, it seems that I need to search one by one.
Thanks for suggestions!
An example list:
Fopnl
AI597479
Ccnb1ip1
Arhgap17
Prmt7
Fbxo11
Plekhg2
Ric1
Trub1
Rfc4
Ric8a
n.R5.8s1
Fbxo6
Med23
Nol4l
Rbsn
Dis3
Ddx23
Mtrf1l
I guess downloading PFAM could work. Question is then how to extract a "ID -> domain annotations" from the full database.
1 answer
You could use BioMart. Help video to get you started. Filter by your list of identifiers, get PFAM domains as attributes.
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show us a few identifiers from your list please.
NCBI CDD is batch query tool for domain searching provided you have the sequences for these identifiers.