How to get a snapshot for the content of some file on Pfam ?
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12 months ago

I want to get data from Pfam website, but I am not sure which file on the FTP site fits my need, and as some files are so big, it is hard for me to download each one to check. I had a look over this link, but still feels I need to have a look over a sample of each file to decide which that need. Thanks in advance

Pfam • 255 views
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get data from Pfam website,

What kind of data?

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Actually, I have a list of Swiss-Prot AC (e.g. Q9NRG9, P49588, etc.) and I want to get the protein domains that correspond to those proteins. If you searched with Q9NRG9 in Pfam, you will find this page, and below the page, there is a table that shows the domains in that protein (here, it is only one that is known (WD40 starting at pos. 235 and end at pos. 273).

So, what I want to get from Pfam is a list of domains with their start and end positions for each Swiss-Prot AC entry in my list BTW, my focus only is the proteins from Homosapien species.

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12 months ago
MatthewP ▴ 940

You need download then gunzip Pfam-A.hmm.gz and Pfam-A.hmm.dat.gz to run Pfam.

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Thanks, I will try it.