1hmmemit(1) HMMER Manual hmmemit(1)
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6 hmmemit - sample sequences from a profile HMM
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10 hmmemit [options] hmmfile
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15 The hmmemit program samples (emit) sequences from the profile HMM in
16 hmmfile, and outputs them. The hmmfile should contain only a single
17 HMM, not a library of them; only the first HMM will be read.
18 The default is to sample a sequence sequence from the core probability
21 model.
22 Sampling sequences may be useful for a variety of purposes, including
25 creating synthetic true positives for benchmarks or tests.
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30 -h Help; print a brief reminder of command line usage and all
31 available options.
32 -c Emit a consensus sequence, instead of sampling a sequence from
35 the profile HMM's probability distribution. The consensus
36 sequence is formed by selecting the maximum probability residue
37 at each match state.
38 -o <f> Direct the output sequences to file <f>, rather than to stdout.
41 -p Sample sequences from the implicit profile, not from the core
44 model. The core model consists only of the homologous states
45 (between the begin and end states of a HMMER Plan7 model). The
46 profile includes the nonhomologous N, C, and J states,
47 local/glocal and uni/multihit algorithm configuration, and the
48 target length model. Therefore sequences sampled from a profile
49 may include nonhomologous as well as homologous sequences, and
50 may contain more than one homologous sequence segment. By
51 default, the profile is in multihit local mode, and the target
52 sequence length is configured for L=400. To change these
53 defaults, see Options Controlling Emission from Profiles, below.
54 -N <n> Sample <n> sequences, rather than just one.
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62 All these options require that the -p option is also set.
63 -L <n> Configure the profile's target sequence length model to generate
67 a mean length of approximately <n> rather than the default of
68 400.
69 --local
72 Configure the profile for multihit local alignment.
73 --unilocal
76 Configure the profile for unihit local alignment (Smith/Water‐
77 man).
78 --glocal
81 Configure the profile for multihit glocal alignment.
82 --uniglocal
85 Configure the profile for unihit glocal alignment.
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90 --seed <n>
91 Seed the random number generator with <n>, an integer >= 0. If
92 <n> is nonzero, any stochastic simulations will be reproducible;
93 the same command will give the same results. If <n> is 0, the
94 random number generator is seeded arbitrarily, and stochastic
95 simulations will vary from run to run of the same command. The
96 default is 0: use an arbitrary seed, so different hmmemit runs
97 will generate different samples.
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105 See hmmer(1) for a master man page with a list of all the individual
106 man pages for programs in the HMMER package.
107 For complete documentation, see the user guide that came with your
110 HMMER distribution (Userguide.pdf); or see the HMMER web page
111 (@HMMER_URL@).
112
117 @HMMER_COPYRIGHT@
118 @HMMER_LICENSE@
119 For additional information on copyright and licensing, see the file
121 called COPYRIGHT in your HMMER source distribution, or see the HMMER
122 web page (@HMMER_URL@).
123
127 Eddy/Rivas Laboratory
128 Janelia Farm Research Campus
129 19700 Helix Drive
130 Ashburn VA 20147 USA
131 http://eddylab.org
132HMMER @HMMER_VERSION@ @HMMER_DATE@ hmmemit(1)