hmm2emit(1)

📦 version 2.3.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ hmm2emit(1) — the HMMER Manual, bestie edition ✨

okay so picture this: it's a hmm2emit(1) page, it lives in the HMMER Manual, and it's about to become your new fave. let's go 💅

🎀 NAME 🎀

hmm2emit — generate sequences from a profile HMM

like, you give it an HMM, it gives you sequences back. iconic behavior honestly 🦋

🌸 SYNOPSIS 🌸

hmm2emit [options] hmmfile

💖 DESCRIPTION 💖

so hmm2emit reads an HMM file from hmmfile, and that file can have one or more HMMs in it (plural, she contains multitudes 💜). then it generates a number of sequences from each HMM.

OR — and this is the plot twist — if you pick the -c option, it generates a single majority-rule consensus instead. periodt.

why would you even want this? because sometimes you need a simulation of sequences that are consistent with a sequence family consensus, and that's useful for various applications. no cap. 🔥

by default, hmm2emit generates 10 sequences and spits them out in FASTA (unaligned) format. that's the whole default vibe. ✨

👑 OPTIONS 👑

  • -a — write the generated sequences in an aligned format (SELEX) instead of FASTA. glow up but make it aligned 💫
  • -c — predict a single majority-rule consensus sequence instead of sampling sequences from the HMM's probability distribution. highly conserved residues (p >= 0.9 for DNA, p >= 0.5 for protein) are shown in upper case; others are shown in lower case. some insert states may become part of the majority rule consensus, because they are used in >= 50% of generated sequences; when this happens, insert-generated residues are simply shown as "x". lowercase is giving shy, uppercase is giving main character energy 😌
  • -h — print brief help; includes the version number and a summary of all options, including expert options. it's the "hi bestie, here's everything" button 🫶
  • -n <n> — generate <n> sequences. default is 10. ✨
  • -o <f> — save the synthetic sequences to file <f> rather than writing them to stdout. like, put them somewhere nice 🎀
  • -q — quiet; suppress all output except for the sequences themselves. useful for piping or directing the output. she's reserved, she's mysterious, she only says what matters 💀

🌈 EXPERT OPTIONS 🌈

  • --seed <n> — set the random seed to <n>, where <n> is a positive integer. the default is to use time() to generate a different seed for each run, which means that two different runs of hmm2emit on the same HMM will give slightly different results. you can use this option to generate reproducible results. so if you want the same sequence twice, this is your girl 🧚
ngl the default randomness is a whole vibe but if you need consistency, --seed is right there. 🍓

🔥 SEE ALSO 🔥

  • Master man page, with full list of and guide to the individual man pages: see hmmer2(1).
  • For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, http://hmmer.janelia.org/.

Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.

Freely distributed under the GNU General Public License (GPL).

See the file COPYING in your distribution for details on redistribution conditions.

⭐ AUTHOR ⭐

Sean Eddy HHMI/Dept. of Genetics Washington Univ. School of Medicine 4566 Scott Ave. St Louis, MO 63110 USA http://www.genetics.wustl.edu/eddy/

and that's the whole page bestie 🫶 this one's from HMMER 2.3.2, dated Oct 2003 — old but gold, fr fr. go generate some sequences, you got this 💅✨

📦 where this page comes from