hmmemit(1) HMMER Manual hmmemit(1)NAMEhmmemit - sample sequences from a profile HMM
SYNOPSIShmmemit [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/Water‐
man).
--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)
