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/
