NAME

       hmmemit - sample sequences from a profile HMM

SYNOPSIS

       hmmemit [options] hmmfile

DESCRIPTION

       The  hmmemit  program  samples  (emits)  sequences from the profile HMM(s) in hmmfile, 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 one unaligned sequence from the core probability model, which means that each
       sequence consists of one full-length domain.  Alternatively, with the -c option, you can  emit  a  simple
       majority-rule  consensus  sequence;  or with the -a option, you can emit an alignment (in which case, you
       probably also want to set -N to something other than its default of 1 sequence per model).

       As another option, with the -p option you can sample a sequence from  a  fully  configured  HMMER  search
       profile.  This  means  sampling  a  `homologous  sequence' by HMMER's definition, including nonhomologous
       flanking sequences, local alignments, and multiple domains per sequence, depending on  the  length  model
       and alignment mode chosen for the profile.

       The hmmfile may contain a library of HMMs, in which case each HMM will be used in turn.

       <hmmfile> may be '-' (dash), which means reading this input from stdin rather than a file.

COMMON OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -o <f> Direct the output sequences to file <f>, rather than to stdout.

       -N <n> Sample <n> sequences per model, rather than just one.

OPTIONS CONTROLLING WHAT TO EMIT

       The  default  is  to  sample N sequences from the core model. Alternatively, you may choose one (and only
       one) of the following alternatives.

       -a     Emit an alignment for each HMM in the hmmfile rather than sampling unaligned sequences  one  at  a
              time.

       -c     Emit  a  plurality-rule  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.

       -C     Emit  a  fancier  plurality-rule consensus sequence than the -c option. If the maximum probability
              residue has p < minl show it as a lower case 'any' residue (n or x); if p >= minl and < minu  show
              it  as  a  lower  case  residue;  and  if p >= minu show it as an upper case residue.  The default
              settings of minu and minl are both 0.0, which means -C gives the same output as -c unless you also
              set minu and minl to what you want.

       -p     Sample unaligned sequences from the implicit search 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.

OPTIONS CONTROLLING EMISSION FROM PROFILES

       These options require that you have set the -p option.

       -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.

OPTIONS CONTROLLING FANCY CONSENSUS EMISSION

       These options require that you have set the -C option.

       --minl <x>
              Sets the minl threshold for showing weakly conserved residues as lower case.  (0 <= x <= 1)

       --minu <x>
              Sets the minu threshold for showing strongly conserved residues as upper case.  (0 <= x <= 1)

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 ().

COPYRIGHT

       Copyright (C) 2015 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 HMMER source
       distribution, or see the HMMER web page ().

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER 3.1b2                                       February 2015                                       hmmemit(1)