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23 lines
884 B
Plaintext
23 lines
884 B
Plaintext
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*********************************************************
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Note on environment variables:
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HMMER reads three environment variables:
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HMMERDB - directory location of HMM databases (e.g. PFAM)
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BLASTDB - directory location of FASTA-formatted sequence databases
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BLASTMAT - directory location of PAM scoring matrices
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If you have installed BLAST, you probably already have these
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environment variables set in system-wide or user-specific
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.cshrc files. They are optional. If they are set up, you
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can simplify command lines to:
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> hmmpfam pfam my.query
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> hmmsearch my.hmm swiss35
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instead of
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> hmmpfam /some/long/path/to/databases/pfam my.query
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> hmmsearch my.hmm /some/long/path/to/databases/swiss35
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Please see the website http://hmmer.wustl.edu/ for more information.
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*********************************************************
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