debian man page for hmmemit

Query: hmmemit

OS: debian

Section: 1

Links: debian man pages   all man pages   forum categories

Format:Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

hmmemit(1)							   HMMER Manual 							hmmemit(1)

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 nonhomol- ogous as well as homologous sequences, and may contain more than one homologous sequence segment. By default, the profile is in mul- tihit 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
HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmemit(1)