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 alignment 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/
