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
consistent 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 conserved 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 reproducible 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 background, 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/