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/