NAME¶
cmemit - sample sequences from a covariance model
SYNOPSIS¶
cmemit [options] <cmfile>
DESCRIPTION¶
The
cmemit program samples (emits) sequences from the covariance model(s)
in
<cmfile>, and writes them to output. Sampling sequences may be
useful for a variety of purposes, including creating synthetic true positives
for benchmarks or tests.
The default is to sample ten unaligned sequence from each CM. Alternatively,
with the
-c option, you can emit a single majority-rule consensus
sequence; or with the
-a option, you can emit an alignment.
The
<cmfile> may contain a library of CMs, in which case each CM
will be used in turn.
<cmfile> may be '-' (dash), which means reading this input from
stdin rather than a file.
For models with zero basepairs, sequences are sampled from the profile HMM
filter instead of the CM. However, since these models will be nearly identical
(unless special options were used in
cmbuild to prevent this), using
the HMM instead of the CM will not change the output in a significant way,
unless the
-l option is used. With
-l, the HMM will be
configured for equiprobable model begin and end positions, while the CM will
not. You can force
cmemit to always sample from the CM with the
--nohmmonly option.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and available options.
- -o <f>
- Save the synthetic sequences to file <f> rather than writing
them to stdout.
- -N <n>
- Generate <n> sequences. The default value for
<n> is 10.
- -u
- Write the generated sequences in unaligned format (FASTA). This is the
default behavior.
- -a
- Write the generated sequences in an aligned format (STOCKHOLM) with
consensus structure annotation rather than FASTA. Other output formats are
possible with the --outformat option.
- -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.
- -e <n>
- Embed the CM emitted sequences in a larger randomly generated sequence of
length <n> generated from an HMM that was trained on real
genomic sequences with various GC contents (the same HMM used by
cmcalibrate). You can use the --iid option to generate 25%
A, C, G, and U sequence instead. The CM emitted sequence will begin at a
random position within the larger sequence and will be included in its
entirety unless the --u5p or --u3p options are used. When
-e is used in combination with --u5p, the CM emitted
sequence will always begin at position 1 of the larger sequence and will
be truncated 5'. When used in combination --u3p the CM emitted
sequence will always end at position <n> of the larger
sequence and will be truncated 3'.
- -l
- Configure the CMs into local mode before emitting sequences. By default
the model will be in global mode. In local mode, large insertions and
deletions are more common than in global mode.
OPTIONS FOR TRUNCATING EMITTED SEQUENCES¶
- --u5p
- Truncate all emitted sequences at a randomly chosen start position
<n>, by only outputting residues beginning at
<n>. A different start point is randomly chosen for each
sequence.
- --u3p
- Truncate all emitted sequences at a randomly chosen end position
<n>, by only outputting residues up to position
<n>. A different end point is randomly chosen for each
sequence.
- --a5p <n>
- In combination with the -a option, truncate the emitted alignment
at a randomly chosen start match position <n>, by only
outputting alignment columns for positions after match state
<n> - 1. <n> must be an integer between 0 and
the consensus length of the model (which can be determined using the
cmstat program. As a special case, using 0 as <n> will
result in a randomly chosen start position.
- --a3p <n>
- In combination with the -a option, truncate the emitted alignment
at a randomly chosen end match position <n>, by only
outputting alignment columns for positions before match state
<n> + 1. <n> must be an integer between 1 and
the consensus length of the model (which can be determined using the
cmstat program). As a special case, using 0 as <n>
will result in a randomly chosen end position.
OTHER OPTIONS¶
- --seed <n>
- Seed the random number generator with <n>, an integer >=
0. If <n> is nonzero, stochastic sampling of sequences will
be reproducible; the same command will give the same results. If
<n> is 0, the random number generator is seeded arbitrarily,
and stochastic samplings will vary from run to run of the same command.
The default seed is 0.
- --iid
- With -e, generate the larger sequences as 25% each A, C, G and U.
- --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.
- --idx <n>
- Specify that the emitted sequences be named starting with
<modelname>.<n>. By default <n> is 1.
- --outformat <s>
- With -a, specify the output alignment format as <s>.
Acceptable formats are: Pfam, AFA, A2M, Clustal, and Phylip. AFA is
aligned fasta. Only Pfam and Stockholm alignment formats will include
consensus structure annotation.
- --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 <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
more difficult ( <x> < 1.0) or easier ( <x>
> 1.0) for the CM to distinguish as homologous from background, random
sequence.
- --hmmonly
- Emit from the filter profile HMM instead of the CM.
- --nohmmonly
- Never emit from the filter profile HMM, always use the CM, even for models
with zero basepairs.
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) 2014 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
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