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Pfam database

Install Pfam database for HMMER
  1. Download and unpack database from ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release (100 MB), for example:

    mkdir /shared/db/pfam; cd /shared/db/pfam
    wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam_ls.gz
    gzip -d Pfam_ls.gz
    
  2. Index the database:

    hmmindex Pfam_ls
    

    Note:

    Indexing will actually be done automatically when you first use hmmsearch or Biskit/Hmmer.py but it may fail then if you don't have write permissions for the database folder.

  3. Configure Biskit

    Edit ~/.biskit/settings.dat and assign the path of the Pfam database file to the 'hmm_db' parameter. Example:

    hmm_db = /shared/db/pfam/Pfam_ls
    
  4. Test Biskit / Hmmer interface:

    cd biskit/Biskit
    python Hmmer.py
    

Usage:
see Hmmer and PDBDope.addConservation()
Custom configuration:

see

  • biskit/external/defaults/exe_hmmpfam.dat