---
name: "cm2hmmsearch"
section: "1"
platform: "linux"
package: "infernal"
version: "1.0.2-2"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/cm2hmmsearch"
---

# cm2hmmsearch(1)

## 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/
```