Query: hmmemit
OS: debian
Section: 1
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hmmemit(1) HMMER Manual hmmemit(1)NAMEhmmemit - sample sequences from a profile HMMSYNOPSIShmmemit [options] hmmfileDESCRIPTIONThe 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 PROFILESAll 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 ALSOSee 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@).AUTHOREddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.orgHMMER@HMMER_VERSION@ @HMMER_DATE@ hmmemit(1)