1hmmemit(1)                       HMMER Manual                       hmmemit(1)
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NAME

6       hmmemit - generate sequences from a profile HMM
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SYNOPSIS

10       hmmemit [options] hmmfile
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DESCRIPTION

14       hmmemit reads an HMM file from hmmfile containing one or more HMMs, and
15       generates a number of sequences from each HMM; or, if the -c option  is
16       selected,  generate a single majority-rule consensus.  This can be use‐
17       ful for various  applications  in  which  one  needs  a  simulation  of
18       sequences consistent with a sequence family consensus.
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20       By  default,  hmmemit  generates 10 sequences and outputs them in FASTA
21       (unaligned) format.
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OPTIONS

25       -a     Write the generated  sequences  in  an  aligned  format  (SELEX)
26              rather than FASTA.
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29       -c     Predict  a  single  majority-rule  consensus sequence instead of
30              sampling sequences  from  the  HMM's  probability  distribution.
31              Highly  conserved  residues (p >= 0.9 for DNA, p >= 0.5 for pro‐
32              tein) are shown in upper case; others are shown in  lower  case.
33              Some  insert states may become part of the majority rule consen‐
34              sus, because they are used in >=  50%  of  generated  sequences;
35              when this happens, insert-generated residues are simply shown as
36              "x".
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39       -h     Print brief help; includes version number  and  summary  of  all
40              options, including expert options.
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43       -n <n> Generate <n> sequences. Default is 10.
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46       -o <f> Save  the  synthetic  sequences  to file <f> rather than writing
47              them to stdout.
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50       -q     Quiet; suppress all output except for the sequences  themselves.
51              Useful for piping or directing the output.
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EXPERT OPTIONS

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

66       Master  man  page,  with  full  list of and guide to the individual man
67       pages: see hmmer(1).
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69       For complete documentation, see the user guide that came with the  dis‐
70       tribution    (Userguide.pdf);    or    see    the   HMMER   web   page,
71       http://hmmer.wustl.edu/.
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75       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
76       Freely distributed under the GNU General Public License (GPL).
77       See the file COPYING in your distribution for details on redistribution
78       conditions.
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AUTHOR

82       Sean Eddy
83       HHMI/Dept. of Genetics
84       Washington Univ. School of Medicine
85       4566 Scott Ave.
86       St Louis, MO 63110 USA
87       http://www.genetics.wustl.edu/eddy/
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93HMMER 2.3.2                        Oct 2003                         hmmemit(1)
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