cmsearch - search a sequence database for RNAs homologous to a CM,
using an HMM as a pre-filtering step to increase speed.
cmsearch window length score threshold cmfile compact-type HMM
expanded-type HMM seqfile runsearch
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.
--help Print brief help; includes summary of parameters.
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.
For complete documentation, see the User’s Guide (Userguide.pdf) that
came with the distribution; or see the Infernal web page,
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
Eric Nawrocki, Diana Kolbe, and Sean Eddy
HHMI Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147