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Pfam database

Install Pfam database for HMMER
  1. Download and unpack database from (100 MB), for example:

    mkdir /shared/db/pfam; cd /shared/db/pfam
    gzip -d Pfam_ls.gz
  2. Index the database:

    hmmindex Pfam_ls


    Indexing will actually be done automatically when you first use hmmsearch or Biskit/ 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

see Hmmer and PDBDope.addConservation()
Custom configuration:


  • biskit/external/defaults/exe_hmmpfam.dat