hmmemit(1) HMMER Manual hmmemit(1)
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 nonhomol-
ogous as well as homologous sequences, and may contain more than one homologous sequence segment. By default, the profile is in mul-
tihit 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
HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmemit(1)
