Mapping from interpro domain-ID to pfam domain in python

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3.1 years ago

d6eada4c • 0

Hi everyone,

I am currently looking into InterPro entries and I would like to convert those to their respective PFam IDs when that exists. Is there an efficient way to go about this? (e.g. via python?)

Thanks a lot for the help!

InterPro PFam Proteins Domains Python • 1.2k views

ADD COMMENT • link 3.1 years ago by d6eada4c • 0

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if you run interpro you will get the pfam domains among them, no? (Pfam is part of the interpro suite of DBs)

ADD REPLY • link 3.1 years ago by lieven.sterck 15k

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Hi,

Yes, but the InterPro IDs were given to me. Did you mean to run something like InterPro scan to obtain the respective PFam IDs?

ADD REPLY • link 3.1 years ago by d6eada4c • 0

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ah, ok.

in that case you can look those IDs on the interpro website which will indicate if and which pfam domain they are based on.

Keep in mind that not all interpro domain IDs will have a pfam domain.

ADD REPLY • link 3.1 years ago by lieven.sterck 15k

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Alright that makes sense, thank you! So I guess the most efficient way to do this is to download the InterPro db as an .xml file and lookup there for the respective pfam ID when one exists ?

ADD REPLY • link 3.1 years ago by d6eada4c • 0

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