Question: Matching Uniprot position to Pfam HMM position
gravatar for agonic
4.5 years ago by
agonic20 wrote:

I have a single sequence position representing an amino acid substitution in a protein for which I have the Uniprot accession and the sequence.

I also retreived the positions (start and end) and identifiers for all Pfam domains present in the protein.

Now I have a dataset that annotates the Pfam HMM profile for each Pfam family with data that I need. Is it possible, given a residue position in a domain within a protein with a Uniprot entry, to find out which position in the Pfam HMM that corresponds to?

pfam snp uniprot • 1.7k views
ADD COMMENTlink written 4.5 years ago by agonic20

Normally if you run Pfam locally, you will get Pfam domain results for your query proteins where Pfam will display your UniProt id and domain position (start and end). Now if you want to see whether your residue present in domain regions then you can write your script to get what you want!!

ADD REPLYlink written 4.5 years ago by Pallab Bhowmick20
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