debian man page for cm2hmmsearch

cmsearch(1)							  Infernal Manual						       cmsearch(1)

NAME
       cmsearch - search a sequence database for RNAs homologous to a CM,
	      using an HMM as a pre-filtering step to increase speed.

SYNOPSIS
       cmsearch window length score threshold cmfile compact-type HMM expanded-type HMM seqfile runsearch

DESCRIPTION
       cm2hmmsearch  uses  the	covariance  model (CM) in cmfile to search for homologous RNAs in seqfile, and outputs high-scoring alignments.  A
       compact-type HMM and/or expanded-type HMM is used as a pre-filtering step, which usually increases the overall speed of the  search.   HMMs
       created with cm2hmm are rigorous, meaning that no new false negatives are introduced by using the filter.

       The sequence file is assumed to be in FASTA format.

       CM  files are profiles of RNA consensus secondary structure. A CM file is produced by the cmbuild program, from a given RNA sequence align-
       ment of known consensus structure.

       HMM files are profiles of RNA consensus primary sequence, produced by cm2hmm from a given CM file.

OPTIONS
       --help Print brief help; includes summary of parameters.

       window length

       score threshold

       runsearch
	      Indicate whether cmsearch should actually be run.  1 will run the cmsearch and output hits.  0 will report on the filtering fraction
	      that was achieved with the HMM filters.

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 						       cmsearch(1)