NAME

       hmm2emit - generate sequences from a profile HMM

SYNOPSIS

       hmm2emit [options] hmmfile

DESCRIPTION

       hmm2emit  reads an HMM file from hmmfile containing one or more HMMs, and generates a number of sequences
       from each HMM; or, if the -c option is selected, generate a single majority-rule consensus.  This can  be
       useful  for  various applications in which one needs a simulation of sequences consistent with a sequence
       family consensus.

       By default, hmm2emit generates 10 sequences and outputs them in FASTA (unaligned) format.

OPTIONS

       -a     Write the generated sequences in an aligned format (SELEX) rather than FASTA.

       -c     Predict a single majority-rule consensus sequence instead of sampling  sequences  from  the  HMM's
              probability  distribution.  Highly conserved residues (p >= 0.9 for DNA, p >= 0.5 for protein) are
              shown in upper case; others are shown in lower case.  Some insert states may become  part  of  the
              majority  rule  consensus,  because  they  are  used  in  >= 50% of generated sequences; when this
              happens, insert-generated residues are simply shown as "x".

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -n <n> Generate <n> sequences. Default is 10.

       -o <f> Save the synthetic sequences to file <f> rather than writing them to stdout.

       -q     Quiet; suppress all output except for the sequences themselves.  Useful for  piping  or  directing
              the output.

EXPERT OPTIONS

       --seed <n>
              Set  the  random  seed  to  <n>,  where <n> is a positive integer. The default is to use time() to
              generate a different seed for each run, which means that two different runs  of  hmm2emit  on  the
              same  HMM  will give slightly different results.  You can use this option to generate reproducible
              results.

SEE ALSO

       Master man page, with full list of and guide to the individual man pages: see hmmer2(1).

       For          complete           documentation,           see           the           user           guide
       (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf);    or   see   the   HMMER   web   page,
       http://hmmer.janelia.org/.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/

HMMER 2.3.2                                         Oct 2003                                         hmm2emit(1)