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Note on environment variables:

   HMMER reads three environment variables:
      HMMERDB  - directory location of HMM databases (e.g. PFAM)
      BLASTDB  - directory location of FASTA-formatted sequence databases
      BLASTMAT - directory location of PAM scoring matrices

   If you have installed BLAST, you probably already have these 
   environment variables set in system-wide or user-specific
   .cshrc files. They are optional. If they are set up, you
   can simplify command lines to:
      > hmmpfam pfam my.query
      > hmmsearch my.hmm swiss35
   instead of
      > hmmpfam   /some/long/path/to/databases/pfam my.query
      > hmmsearch my.hmm /some/long/path/to/databases/swiss35

Please see the website http://hmmer.wustl.edu/ for more information.

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