sse_cmsearch(1)

NAME

sse_cmsearch - search covariance models against a sequence database using an SSE implementation

SYNOPSIS
sse_cmsearch [options] <cmfile> <seqdb>

DESCRIPTION
sse_cmsearch uses the covariance model (CM) in <cmfile> to search for homologous RNAs in <seqdb>, and outputs high-scoring alignments, using a structural filter pipeline implemented with SSE parallel code.

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 sse_cmsearch with the cmcalibrate program.

sse_cmsearch output is designed for processing by the cmsearch_dual script; --glbf 3 gives coordinates and scores of the final results list.

OPTIONS

-h  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.

--toponly
    Only search the top (Watson) strand of the sequences in <seqdb>. By default, both strands are searched. This will halve the database size (Z).

--s1-F <x>
    Set stage 1 cutoff to estimated filter pass rate <x>, where <x> is a real number between 0 and 1.

--s2-P <x>
    Set stage 2 cutoff to a p-value of <x>, where <x> is a real number between 0 and 1.

--s3-E <x>
    Set stage 2 cutoff to a e-value of <x>, where <x> is a positive real number.

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