Man Linux: Main Page and Category List


       hmmemit - generate sequences from a profile HMM


       hmmemit [options] hmmfile


       hmmemit 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,  hmmemit  generates 10 sequences and outputs them in FASTA
       (unaligned) format.


       -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.


       --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 hmmemit on the same
              HMM will give slightly different  results.   You  can  use  this
              option to generate reproducible results.


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

       For complete documentation, see the  user  guide  that  came  with  the
       distribution    (Userguide.pdf);   or   see   the   HMMER   web   page,


       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


       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA