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 (emits) sequences from the profile HMM(s)
16 in hmmfile, and writes them to output. Sampling sequences may be use‐
17 ful for a variety of purposes, including creating synthetic true posi‐
18 tives for benchmarks or tests.
19 The default is to sample one unaligned sequence from the core probabil‐
22 ity model, which means that each sequence consists of one full-length
23 domain. Alternatively, with the -c option, you can emit a simple
24 majority-rule consensus sequence; or with the -a option, you can emit
25 an alignment (in which case, you probably also want to set -N to some‐
26 thing other than its default of 1 sequence per model).
27 As another option, with the -p option you can sample a sequence from a
30 fully configured HMMER search profile. This means sampling a `homolo‐
31 gous sequence' by HMMER's definition, including nonhomologous flanking
32 sequences, local alignments, and multiple domains per sequence, depend‐
33 ing on the length model and alignment mode chosen for the profile.
34 The hmmfile may contain a library of HMMs, in which case each HMM will
37 be used in turn.
38 <hmmfile> may be '-' (dash), which means reading this input from stdin
41 rather than a file.
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46 -h Help; print a brief reminder of command line usage and all
47 available options.
48 -o <f> Direct the output sequences to file <f>, rather than to stdout.
52 -N <n> Sample <n> sequences per model, rather than just one.
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60 The default is to sample N sequences from the core model. Alterna‐
61 tively, you may choose one (and only one) of the following alterna‐
62 tives.
63 -a Emit an alignment for each HMM in the hmmfile rather than sam‐
67 pling unaligned sequences one at a time.
68 -c Emit a plurality-rule consensus sequence, instead of sampling a
71 sequence from the profile HMM's probability distribution. The
72 consensus sequence is formed by selecting the maximum probabil‐
73 ity residue at each match state.
74 -C Emit a fancier plurality-rule consensus sequence than the -c
77 option. If the maximum probability residue has p < minl show it
78 as a lower case 'any' residue (n or x); if p >= minl and < minu
79 show it as a lower case residue; and if p >= minu show it as an
80 upper case residue. The default settings of minu and minl are
81 both 0.0, which means -C gives the same output as -c unless you
82 also set minu and minl to what you want.
83 -p Sample unaligned sequences from the implicit search profile, not
86 from the core model. The core model consists only of the homol‐
87 ogous states (between the begin and end states of a HMMER Plan7
88 model). The profile includes the nonhomologous N, C, and J
89 states, local/glocal and uni/multihit algorithm configuration,
90 and the target length model. Therefore sequences sampled from a
91 profile may include nonhomologous as well as homologous
92 sequences, and may contain more than one homologous sequence
93 segment. By default, the profile is in multihit local mode, and
94 the target sequence length is configured for L=400.
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101 These options require that you have set the -p option.
102 -L <n> Configure the profile's target sequence length model to generate
105 a mean length of approximately <n> rather than the default of
106 400.
107 --local
110 Configure the profile for multihit local alignment.
111 --unilocal
114 Configure the profile for unihit local alignment (Smith/Water‐
115 man).
116 --glocal
119 Configure the profile for multihit glocal alignment.
120 --uniglocal
123 Configure the profile for unihit glocal alignment.
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128 These options require that you have set the -C option.
129 --minl <x>
132 Sets the minl threshold for showing weakly conserved residues as
133 lower case. (0 <= x <= 1)
134 --minu <x>
137 Sets the minu threshold for showing strongly conserved residues
138 as upper case. (0 <= x <= 1)
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144 --seed <n>
145 Seed the random number generator with <n>, an integer >= 0. If
146 <n> is nonzero, any stochastic simulations will be reproducible;
147 the same command will give the same results. If <n> is 0, the
148 random number generator is seeded arbitrarily, and stochastic
149 simulations will vary from run to run of the same command. The
150 default is 0: use an arbitrary seed, so different hmmemit runs
151 will generate different samples.
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159 See hmmer(1) for a master man page with a list of all the individual
160 man pages for programs in the HMMER package.
161 For complete documentation, see the user guide that came with your
164 HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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170 Copyright (C) 2015 Howard Hughes Medical Institute.
171 Freely distributed under the GNU General Public License (GPLv3).
172 For additional information on copyright and licensing, see the file
174 called COPYRIGHT in your HMMER source distribution, or see the HMMER
175 web page ().
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180 Eddy/Rivas Laboratory
181 Janelia Farm Research Campus
182 19700 Helix Drive
183 Ashburn VA 20147 USA
184 http://eddylab.org
185HMMER 3.1b2 February 2015 hmmemit(1)