cm2hmmsearch1
Usage
cmsearch window
length
score
threshold
cmfile
compact-type
HMM
expanded-type
HMM
seqfile
runsearch
Overview
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.
Releases
Unchanged in 2 releases since Debian 6.0 (Squeeze).