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How to extract all Pfam Sequences with cleared PDB Structure?

I downloaded and extracted the Pfam-A.full.ncbi.gz from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/

I splittet the huge file into smaller files for each family like: https://www.dropbox.com/sh/t0b173oa8odvsne/AABZLhiaq-jZtE5PrULvBm9na?dl=0

Now i try to extract all Sequences from the Alignment, which have an observed/cleared structures in the pdb database. Luckily Pfam provides the pdbmap file which, links pdb IDs to Pfam IDs. I can extract all Pfam families, which have observed structures in the pdb, but i can not extract the corresponding sequences. So any help on how to accomplish this is very appreciated.

PS: I currently use Python 2.7 with BioPython, but it can't handle the files.

python pfam pdb
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written by twinstar2 • twinstar2

1 answer

Okay for anyone with the same problem, i found the answer!

  1. Extract all UniProtKB ids (line 5) from the pdbmap file into a list (you may have to make smaller sub parts of the list due to Server limitations)
  2. Upload the List here: http://www.uniprot.org/mapping/ and select "UniProtKB AC/ID" as Input and "EMBL/GenBank/DDBJ CDS" as Output
  3. Rejoin the target_id list
  4. Iterate over all Pfam files and dump all sequences which are not in your targed_id list
  5. Let it run for 2 days
  6. ????
  7. profit

This will get you ~ 70.000 sequences

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written by twinstar2 • twinstar2

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