Man Linux: Main Page and Category List


       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.

       window length

       score threshold

              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
       redistribution conditions.


       Eric Nawrocki, Diana Kolbe, and Sean Eddy
       HHMI Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147