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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 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

HMMER @HMMER_VERSION@            @HMMER_DATE@                       hmmemit(1)

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