cmsearch_dual(1)

NAME

cmsearch_dual - search covariance model(s) against a sequence database using two filter pipelines

SYNOPSIS
cmsearch_dual [options] <cmfile> <seqdb>

DESCRIPTION
cmsearch_dual uses the covariance model (CM) in <cmfile> to search for homologous RNAs in <seqdb>, and outputs high-scoring alignments. cmsearch_dual runs both the standard filter pipeline of cmsearch and the structure-based filter pipeline of sse_cmsearch and combines the results in a single, sorted results list.

Currently, the sequence file must be in FASTA format.

CMs are profiles of RNA consensus sequence and secondary structure. A CM file is produced by the cmbuild program, from a given RNA sequence alignment of known consensus structure. CM files must be calibrated prior to running cmsearch_dual with the cmcalibrate program.

cmsearch_dual output is in the same format used by cmsearch; consult the user guide for more detail.

OPTIONS

--help
    Print brief help, including summary of available options.

-Z <x>
    Calculate E-values as if the target database size was <x> megabases (Mb). Without the use of this option, the search space size is defined as the total number of nucleotides in <seqdb> times 2, because both strands of each target sequence will be searched.

-P <n>
    Directly specify the path <n> to cmsearch. This is unecessary if cmsearch is installed and available in your path.

-Q <n>
    Directly specify the path <n> to sse_cmsearch. This is usually necessary because sse_cmsearch is not installed by Infernal, but it is built on systems with SSE parallelization capability. It can be found in the src/impl_sse/ directory.

-R <n>
    Directly specify the path <n> to esl-sfetch. This is unecessary if esl-sfetch is installed and available in your path.

SEE ALSO
See infernal(1) for a master man page with a list of all the individual man pages for programs in the Infernal package.

For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page ().

COPYRIGHT
Copyright (C) 2019 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the Infernal web page ().

AUTHOR
The Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org