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) 2013 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