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/