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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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