NAME¶
hmmemit - sample sequences from a profile HMM
SYNOPSIS¶
hmmemit [options] hmmfile
DESCRIPTION¶
The
hmmemit program samples (emit) sequences from the profile HMM in
hmmfile, and outputs them. The
hmmfile should contain only a
single HMM, not a library of them; only the first HMM will be read.
The default is to sample a sequence sequence from the core probability model.
Sampling sequences may be useful for a variety of purposes, including creating
synthetic true positives for benchmarks or tests.
COMMON OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all
available options.
- -c
- Emit a consensus sequence, instead of sampling a sequence
from the profile HMM's probability distribution. The consensus sequence is
formed by selecting the maximum probability residue at each match state.
- -o <f>
- Direct the output sequences to file <f>,
rather than to stdout.
- -p
- Sample sequences from the implicit profile, not from the
core model. The core model consists only of the homologous states (between
the begin and end states of a HMMER Plan7 model). The profile includes the
nonhomologous N, C, and J states, local/glocal and uni/multihit algorithm
configuration, and the target length model. Therefore sequences sampled
from a profile may include nonhomologous as well as homologous sequences,
and may contain more than one homologous sequence segment. By default, the
profile is in multihit local mode, and the target sequence length is
configured for L=400. To change these defaults, see Options Controlling
Emission from Profiles, below.
- -N <n>
- Sample <n> sequences, rather than just one.
OPTIONS CONTROLLING EMISSION FROM PROFILES¶
All these options require that the
-p option is also set.
- -L <n>
- Configure the profile's target sequence length model to
generate a mean length of approximately <n> rather than the default
of 400.
- --local
- Configure the profile for multihit local alignment.
- --unilocal
- Configure the profile for unihit local alignment
(Smith/Waterman).
- --glocal
- Configure the profile for multihit glocal alignment.
- --uniglocal
- Configure the profile for unihit glocal alignment.
OTHER OPTIONS¶
- --seed <n>
- Seed the random number generator with <n>, an
integer >= 0. If <n> is nonzero, any stochastic
simulations will be reproducible; the same command will give the same
results. If <n> is 0, the random number generator is seeded
arbitrarily, and stochastic simulations will vary from run to run of the
same command. The default is 0: use an arbitrary seed, so different
hmmemit runs will generate different samples.
SEE ALSO¶
See
hmmer(1) for a master man page with a list of all the individual man
pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your HMMER
distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@).
COPYRIGHT¶
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page
(@HMMER_URL@).
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org