cm2hmm(1) [debian man page]

cm2hmm(1)							  Infernal Manual							 cm2hmm(1)

NAME

       cm2hmm - build a rigorous HMM-based filter from an existing covariance model (CM)

SYNOPSIS

       cm2hmm cmfile hmmfile background [background parameters] HMMtype optimizer [optimizer parameters]

DESCRIPTION

       cm2hmm  reads  a  covariance  model  (CM) from cmfile, constructs a hidden-Markov model (HMM) that preserves some information of the CM and
       saves the HMM to hmmfile.  The HMM can be used as a rigorous pre-filtering step to searching with the CM.

       The CM file must be in the standard format output used by Infernal.

OPTIONS

       --help Print brief help; includes summary of command-line parameters.

       background [background parameters]
	      Select the model of background sequence.	uniform gives all bases equal probability (25%).  gc <fraction> specifies the G+C content.
	      <fraction> should be a number between 0 and 1.  file <filename> loads the base distribution from a file in a specific format.

       HMMtype
	      Specify  the  type of HMM to be used; options are compact and expanded.  Compact-type models are generally faster, but expanded-type
	      models may provide better filtering.

       optimizer [optimizer parameters]
	      Specify which mathematical optimizer is to be used to create the final model.  Currently the only option is cfsqp  which	takes  two
	      paramters: <B> <C>.  B=0, C=1 are reasonable choices.  (See the CFSQP manual for further details.)

SEE ALSO

       For  complete  documentation,  see  the	User's	Guide  (Userguide.pdf)	that  came  with  the  distribution; or see the Infernal web page,
       http://infernal.janelia.org/.

COPYRIGHT

       Copyright (C) 2009 HHMI Janelia Farm Research Campus.
       Freely distributed under the GNU General Public License (GPLv3).
       See the file COPYING that came with the source for details on redistribution conditions.

AUTHOR

       Eric Nawrocki, Diana Kolbe, and Sean Eddy
       HHMI Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147
       http://selab.janelia.org/

Infernal 1.0.2							   October 2009 							 cm2hmm(1)

hmmfetch(1)							   HMMER Manual 						       hmmfetch(1)

NAME

       hmmfetch - retrieve profile HMM(s) from a file

SYNOPSIS

       hmmfetch [options] <hmmfile> <key>
	(retrieves HMM named <key>)

       hmmfetch -f [options] <hmmfile> <keyfile>
	(retrieves all HMMs listed in <keyfile>)

       hmmfetch --index [options] <hmmfile>
	(indexes <hmmfile> for fetching)

DESCRIPTION

       Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for example).

       The <hmmfile> must be indexed first, using hmmfetch --index.  The index is a binary file named <hmmfile>.ssi.

       The default mode is to retrieve a single profile by name or accession, called the <key>.  For example:

	 % hmmfetch Pfam-A.hmm Caudal_act
	 % hmmfetch Pfam-A.hmm PF00045

       With  the  -f option, a <keyfile> containing a list of one or more keys is read instead.  The first whitespace-delimited field on each non-
       blank non-comment line of the <keyfile> is used as a <key>, and any remaining data on the line is ignored; this allows a variety of  white-
       space  delimited  datafiles  to	be used as <keyfile>s.	The <keyfile> argument can be a '-' (dash) character, in which case the keyfile is
       read from standard input; this allows unix ninjas to construct sophisticated invocations using pipes.

       By default, the HMM is printed to standard output in HMMER3 format.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -f     The second commandline argument is a <keyfile> instead of a single <key>.  The first field on each line of the <keyfile> is used	as
	      a retrieval <key> (an HMM name or accession).  Blank lines and comment lines (that start with a # character) are ignored.

       -o <f> Output HMM(s) to file <f> instead of to standard output.

       -O     Output  HMM(s) to individual file(s) named <key> instead of standard output. With the -f option, this can result in many files being
	      created.

       --index
	      Instead of retrieving one or more profiles from <hmmfile>, index the <hmmfile> for future retrievals.  This creates a  <hmmfile>.ssi
	      binary index file.

SEE ALSO

       See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

       For  complete  documentation,  see  the	user  guide  that  came  with  your  HMMER distribution (Userguide.pdf); or see the HMMER web page
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or  see	the  HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						       hmmfetch(1)