Where can I download ALL pfam flat-file annotations?
I tried downloading the following: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/mappings/pdb_pfam_mapping.txt
but it's missing a huge number of PFAM ids. For example, PF13276 isn't in there. Is there another place where I can get these flatfiles?
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mwylerCH •
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The Pfam-A.hmm.dat.gz file contains the required informations. Each entry looks like:
# STOCKHOLM 1.0
#=GF ID ZZ
#=GF AC PF00569.20
#=GF DE Zinc finger, ZZ type
#=GF GA 21.4; 21.4;
#=GF TP Domain
#=GF ML 45
#=GF CL CL0006
alternatively a shorter version is available in the Pfam-A.clans.tsv.gz file
PF00569 CL0006 C1 ZZ Zinc finger, ZZ type
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perhaps from the PFAM website ? on their ftp site look in to the 'current_release' folder.
I only found one file with annotations ^^^. Do you know if there is another file on the ftp site?
Not without looking into them, but these notes might be informative?
What do you mean with "annotations" btw?
I essentially want to get the name and description given a pfam identifier. For example,
'PF01565': {'NAME': 'FAD_binding_4', 'DESCRIPTION': 'FAD binding domain'}