1hmmfetch(1)                      HMMER Manual                      hmmfetch(1)
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NAME

6       hmmfetch - retrieve an HMM from an HMM database
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SYNOPSIS

10       hmmfetch [options] database name
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DESCRIPTION

14       hmmfetch  is  a  small utility that retrieves an HMM called name from a
15       HMMER model database called database.  in a new format, and prints that
16       model to standard output.  For example, hmmfetch Pfam rrm retrieves the
17       RRM (RNA recognition motif) model from Pfam, if the  environment  vari‐
18       able  HMMERDB  is  set  to  the  location  of  the  Pfam database.  The
19       retrieved HMM file is written in HMMER 2 ASCII format.
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22       The database must have an associated GSI index file.  To index  an  HMM
23       database, use the program hmmindex.
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OPTIONS

27       -h     Print  brief  help;  includes  version number and summary of all
28              options, including expert options.
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31       -n     Interpret name as an HMM number instead  of  a  name.  Numbering
32              starts  at  0.   For example, to fetch the first HMM from an HMM
33              database called foo, you would do hmmfetch -n 0 foo.
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SEE ALSO

38       Master man page, with full list of and  guide  to  the  individual  man
39       pages: see hmmer(1).
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41       For  complete documentation, see the user guide that came with the dis‐
42       tribution   (Userguide.pdf);   or   see    the    HMMER    web    page,
43       http://hmmer.wustl.edu/.
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47       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
48       Freely distributed under the GNU General Public License (GPL).
49       See the file COPYING in your distribution for details on redistribution
50       conditions.
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AUTHOR

54       Sean Eddy
55       HHMI/Dept. of Genetics
56       Washington Univ. School of Medicine
57       4566 Scott Ave.
58       St Louis, MO 63110 USA
59       http://www.genetics.wustl.edu/eddy/
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65HMMER 2.3.2                        Oct 2003                        hmmfetch(1)
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