SYNOPSIShmmemit [options] hmmfile
The hmmemit program samples (emits) sequences from the profile HMM(s) in hmmfile, and writes them to output. Sampling sequences may be useful for a variety of purposes, including creating synthetic true positives for benchmarks or tests.
The default is to sample one unaligned sequence from the core probability model, which means that each sequence consists of one full-length domain. Alternatively, with the -c option, you can emit a simple majority-rule consensus sequence; or with the -a option, you can emit an alignment (in which case, you probably also want to set -N to something other than its default of 1 sequence per model).
As another option, with the -p option you can sample a sequence from a fully configured HMMER search profile. This means sampling a `homologous sequence' by HMMER's definition, including nonhomologous flanking sequences, local alignments, and multiple domains per sequence, depending on the length model and alignment mode chosen for the profile.
The hmmfile may contain a library of HMMs, in which case each HMM will be used in turn.
<hmmfile> may be '-' (dash), which means reading this input from stdin rather than a file.
Help; print a brief reminder of command line usage and all available
- -o <f>
Direct the output sequences to file
rather than to
- -N <n>
sequences per model, rather than just one.
OPTIONS CONTROLLING WHAT TO EMIT
The default is to sample N sequences from the core model. Alternatively, you may choose one (and only one) of the following alternatives.
Emit an alignment for each HMM in the
rather than sampling unaligned sequences one at a time.
Emit a plurality-rule consensus sequence, instead of sampling a
sequence from the profile HMM's probability distribution. The
consensus sequence is formed by selecting the maximum probability
residue at each match state.
Emit a fancier plurality-rule consensus sequence than the
option. If the maximum probability residue has p <
show it as a lower case 'any' residue (n or x); if p >=
show it as a lower case residue; and if p >=
show it as an upper case residue.
The default settings of
are both 0.0, which means
gives the same output as
unless you also set
to what you want.
Sample unaligned sequences from the implicit search profile, not from
the core model. The core model consists only of the homologous states
(between the begin and end states of a HMMER Plan7 model). The profile
includes the nonhomologous N, C, and J states, local/glocal and
uni/multihit algorithm configuration, and the target length model.
Therefore sequences sampled from a profile may include nonhomologous
as well as homologous sequences, and may contain more than one
homologous sequence segment. By default, the profile is in multihit
local mode, and the target sequence length is configured for L=400.
OPTIONS CONTROLLING EMISSION FROM PROFILES
These options require that you have set the -p option.
- -L <n>
Configure the profile's target sequence length model to generate a
mean length of approximately <n> rather than the default of 400.
Configure the profile for multihit local alignment.
Configure the profile for unihit local alignment (Smith/Waterman).
Configure the profile for multihit glocal alignment.
Configure the profile for unihit glocal alignment.
OPTIONS CONTROLLING FANCY CONSENSUS EMISSION
These options require that you have set the -C option.
- --minl <x>
threshold for showing weakly conserved residues as lower case.
(0 <= x <= 1)
- --minu <x>
threshold for showing strongly conserved residues as upper case.
(0 <= x <= 1)
- --seed <n>
Seed the random number generator with
an integer >= 0.
is nonzero, any stochastic simulations will be reproducible; the same
command will give the same results.
is 0, the random number generator is seeded arbitrarily, and
stochastic simulations will vary from run to run of the same command.
The default is 0: use an arbitrary seed, so different
runs will generate different samples.
Copyright (C) 2015 Howard Hughes Medical Institute. Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
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