NAME
hmmemit - generate sequences from a profile HMM
SYNOPSIS
hmmemit [options] hmmfile
DESCRIPTION
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.
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 hmmemit 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 hmmer(1).
For complete documentation, see the user guide that came with the
distribution (Userguide.pdf); or see the HMMER web page,
http://hmmer.wustl.edu/.
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/