cmemit(1)							  Infernal Manual							 cmemit(1)

NAME

       cmemit - generate sequences from a covariance model

SYNOPSIS

       cmemit [options] cmfile seqfile

DESCRIPTION

       cmemit  reads  the covariance model(s) (CMs) in cmfile and generates a number of sequences from the CM(s); or if the -c option is selected,
       generates a single majority-rule consensus. This can be useful for various application in which one needs a simulation of sequences consis-
       tent with a sequence family consensus. By default, cmemit generates 10 sequences and outputs them in FASTA (unaligned) format to seqfile.

GENERAL OPTIONS

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -o <f> Save the synthetic sequences to file <f> rather than writing them to stdout.

       -n <n> Generate <n> sequences. Default is 10.

       -u     Write the generated sequences in unaligned format (FASTA). This is the default, so this option is probably useless.

       -a     Write the generated sequences in an aligned format (STOCKHOLM) with consensus structure annotation rather than FASTA.

       -c     Predict  a single majority-rule consensus sequence instead of sampling sequences from the CM's probability distribution. Highly con-
	      served residues (base paired residues that score higher than 3.0 bits, or single stranded residues that score higher than 1.0  bits)
	      are shown in upper case; others are shown in lower case.

       -l     Configure the CMs into local mode before emitting sequences. See the User's Guide for more information on locally configured CMs.

       -s <n> Set the random seed to <n>, where <n> is a positive integer. The default is to use time() to generate a different seed for each run,
	      which means that two different runs of cmemit on the same CM will give different results. You can use this option to generate repro-
	      ducible results.

       --devhelp
	      Print  help, as with -h , but also include undocumented developer options. These options are not listed below, are under development
	      or experimental, and are not guaranteed to even work correctly. Use developer options at your  own  risk.  The  only  resources  for
	      understanding what they actually do are the brief one-line description printed when --devhelp is enabled, and the source code.

EXPERT OPTIONS

       --rna  Specify that the emitted sequences be output as RNA sequences. This is true by default.

       --dna  Specify that the emitted sequences be output as DNA sequences. By default, the output alphabet is RNA.

       --tfile <f>
	      Dump tabular sequence parsetrees (tracebacks) for each emitted sequence to file <f>.  Primarily useful for debugging.

       --exp <x>
	      Exponentiate  the  emission  and	transition probabilities of the CM by <x> and then renormalize those distributions before emitting
	      sequences. This option changes the CM probability distribution of parsetrees relative to default. With <x> less than 1.0 the emitted
	      sequences  will  tend  to  have  lower  bit  scores  upon  alignment to the CM with cmalign.  With <x> greater than 1.0, the emitted
	      sequences will tend to have higher bit scores upon alignment to the CM. This bit score difference will increase as <x> moves further
	      away  from  1.0  in  either direction.  If <x> equals 1.0, this option has no effect relative to default.  This option is useful for
	      generating sequences that are either difficult ( <x> < 1.0) or easy ( <x> > 1.0) for the CM to distinguish as homologous from  back-
	      ground, random sequence.

       --begin <n>
	      Truncate	the  resulting	alignment by removing all residues before consensus column <n>, where <n> is a positive integer no greater
	      than the consensus length of the CM. Must be used in combination with --end and either -a or --shmm (a developer option).

       --end <n>
	      Truncate the resulting alignment by removing all residues after consensus column <n>, where <n> is a  positive  integer  no  greater
	      than the consensus length of the CM. Must be used in combination with --begin and either -a or --shmm (a developer option).

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/

Infernal 1.0.2							   October 2009 							 cmemit(1)