hmmemit(1)

💖 hmmemit — bestie, it's literally a sequence printer 💖

okay so this is the hmmemit(1) page from the HMMER Manual, and we're gonna get you fluent in it, no cap.

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✨ NAME ✨

hmmemit — sample sequences from a profile 🧚

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🌸 SYNOPSIS 🌸

hmmemit [options] hmmfile

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🦋 DESCRIPTION 🦋

So hmmemit takes the profile HMM(s) chilling in hmmfile and samples (aka emits) sequences from them, then writes those sequences to output. Why would you even want that? Because making synthetic true positives for benchmarks or tests is lowkey iconic, that's why. 💅

The default vibe is: sample one unaligned sequence from the core probability model, which means each sequence is one full-length domain. Periodt.

But wait, there's more, and it's giving options:

• With -c, you can emit a simple majority-rule consensus sequence instead.
• With -a, you can emit an alignment — and if you do that, you probably also wanna set -N to something other than its default of 1 sequence per model.
• With -p, you can sample a sequence from a fully configured HMMER search profile. That means you're sampling a homologous sequence by HMMER's definition, including nonhomologous flanking sequences, local alignments, and multiple domains per sequence — all depending on the length model and alignment mode you chose for the profile. main character energy honestly.

Now, hmmfile can totally contain a library of HMMs, in which case each HMM gets used in turn. Slay.

And hmmfile may be '-' (dash), which means read this input from stdin rather than a file. 🫶

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🎀 COMMON OPTIONS 🎀

• -h — Help; print a brief reminder of command line usage and all available options. (your bestie when you're lost, fr)
• -o <f> — Direct the output sequences to file <f>, rather than to stdout.
• -N <n> — Sample <n> sequences per model, rather than just one.

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🌈 OPTIONS CONTROLLING WHAT TO EMIT 🌈

The default is to sample N sequences from the core model. Alternatively, you may choose one (and only one) of the following alternatives. Not two, bestie. One. 🙈

• -a — Emit an alignment for each HMM in the hmmfile rather than sampling unaligned sequences one at a time.
• -c — Emit a plurality-rule 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.
• -C — Emit a fancier plurality-rule consensus sequence than the -c option. Here's the tea: if the maximum probability residue has p < minl, show it as a lower case 'any' residue (n or x); if p >= minl and < minu, show it as a lower case residue; and if p >= minu, show it as an upper case residue. The default settings of minu and minl are both 0.0, which means -C gives the same output as -c unless you also set minu and minl to what you want. 😭
• -p — Sample unaligned sequences from the implicit search 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.

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💜 OPTIONS CONTROLLING EMISSION FROM PROFILES 💜

These options require that you have set the -p option. No -p, no party. 🎈

• -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.

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🌸 OPTIONS CONTROLLING FANCY CONSENSUS EMISSION 🌸

These options require that you have set the -C option. Yes, -C. Capital C. We're being fancy today. 💅

• --minl <x> — Sets the minl threshold for showing weakly conserved residues as lower case. (0 <= x <= 1)
• --minu <x> — Sets the minu threshold for showing strongly conserved residues as upper case. (0 <= x <= 1)

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⭐ 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. 🎲

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👑 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 (http://hmmer.org/).

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🫶 COPYRIGHT 🫶

Copyright (C) 2023 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (http://hmmer.org/).

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💖 AUTHOR 💖

http://eddylab.org

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and that's the whole page, bestie — brought to you by HMMER 3.4, dated Aug 2023, authored by the legends over at http://eddylab.org, and catalogued as hmmemit(1) in the HMMER Manual. go emit some sequences, you absolute icon 🦋✨