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hmmemit

NAME

hmmemit - sample sequences from a profile HMM

SYNOPSIS

hmmemit [options] hmmfile

DESCRIPTION

The hmmemit program samples (emit) sequences from the profile HMM in hmmfile, and outputs them. The hmmfile should contain only a single HMM, not a library of them; only the first HMM will be read.

The default is to sample a sequence sequence from the core probability model.

Sampling sequences may be useful for a variety of purposes, including creating synthetic true positives for benchmarks or tests.

COMMON OPTIONS

-h

Help; print a brief reminder of command line usage and all available options.

-c

Emit a 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.

-o <f>

Direct the output sequences to file <f>, rather than to stdout.

-p

Sample sequences from the implicit 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. To change these defaults, see Options Controlling Emission from Profiles, below.

-N <n>

Sample <n> sequences, rather than just one.

OPTIONS CONTROLLING EMISSION FROM PROFILES

All these options require that the -p option is also set.

-L <n>

Configure the profile's target sequence length model to generate a mean length of approximately <n> rather than the default of 400.

--local

Configure the profile for multihit local alignment.

--unilocal

Configure the profile for unihit local alignment (Smith/Waterman).

--glocal

Configure the profile for multihit glocal alignment.

--uniglocal

Configure the profile for unihit glocal alignment.

OTHER OPTIONS

--seed <n>

Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero, any stochastic simulations will be reproducible; the same command will give the same results. If <n> 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 hmmemit runs will generate different samples.

SEE ALSO

See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

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

COPYRIGHT

 @HMMER_COPYRIGHT@
 @HMMER_LICENSE@
 

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@).

AUTHOR

 Eddy/Rivas Laboratory
 Janelia Farm Research Campus
 19700 Helix Drive
 Ashburn VA 20147 USA
 http://eddylab.org