Infernal(1)

✨ Infernal — the manual page, bestie edition ✨

okay so you opened Infernal(1), which is the summary page for the whole Infernal Manual, and honestly? it's giving iconic. sit down, hydrate, let's go 💅

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🌸 NAME 🌸

Infernal — sequence analysis using profiles of RNA sequence and secondary structure consensus

like. it does RNA. with structure. and vibes. 🦋

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🎀 SYNOPSIS 🎀

cmalign
  Align sequences to a covariance model

cmbuild
  Construct covariance model(s) from structurally annotated RNA multiple
sequence alignment(s)

cmcalibrate
  Fit exponential tails for covariance model E-value determination

cmconvert
  Convert Infernal covariance model files

cmemit
  Sample sequences from a covariance model

cmfetch
  Retrieve covariance model(s) from a file

cmpress
  Prepare a covariance model database for cmscan

cmscan
  Search sequence(s) against a covariance model database

cmsearch
  Search covariance model(s) against a sequence database

cmstat
  summary statistics for a covariance model file

ten little programs. one big slay. 👑

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💖 DESCRIPTION 💖

Infernal is a whole suite of several programs for structural RNA sequence alignment and database homology search. it uses probabilistic models called "covariance models" (CMs) to represent the likely evolutionary homologs of a multiple alignment (or a single sequence, no pressure) of a structural RNA sequence family. yes bestie, covariance. not just a vibe, a whole mathematical situation. 😌

along with the Rfam database of RNA families and the associated CMs (http://rfam.sanger.ac.uk), Infernal can be used to annotate homologs of known structural RNA families in genomes. it's basically the "who are you and why do you look like my family" of RNA. 🔍

Infernal is closely related to the HMMER software suite for sequence family analysis using profile HMMs (http://hmmer.org) — they're cousins, fr fr — but Infernal is designed specifically for structural RNA sequence families. so like, HMMER models the conserved sequence of a family, and CMs do that too, but CMs also model the family's conserved, well-nested (non-pseudoknotted) secondary structure. the way that extra structure is right there 💀

consequence of that though: CM search and alignment methods are relatively computationally expensive. like, highkey expensive. but Infernal uses profile HMMs as filters and for deriving constraints to make the CM methods more practical — so it's not out here rawdogging compute, it's being smart about it. 🧠✨

🌈 the three main modes 🌈

Infernal is used in three main modes, and they're all main character energy:

1. to search a sequence database for new homologs of an RNA family (or annotate homologs in a genome);
2. to search a CM database (like Rfam) to find what known family a query sequence belongs to;
3. and to automatically construct large multiple alignments — i.e. with an effectively unlimited number of sequences — using a CM representative of a sequence family.

🦋 scenario one: you have an alignment, you want more homologs 🦋

suppose you have a structurally annotated multiple sequence alignment of a RNA sequence family of interest, and you want to search a sequence database for additional homologs. okay so:

• the cmbuild program builds covariance model(s) from multiple alignment(s);
• and cmcalibrate determines important parameters for estimating the statistical significance of database hits to the model in subsequent searches.

then cmsearch searches CM(s) against a sequence database. that's the whole pipeline, periodt. 🔥

🍓 scenario two: you have sequences, you want to know the family 🍓

suppose you have sequence(s) that you want to analyze using an Infernal-based CM database like Rfam (http://rfam.sanger.ac.uk). then:

• cmpress formats a covariance model — such as the file you would download from Rfam — into an Infernal binary database;
• and cmscan searches sequence(s) against that database.

download, press, scan. so easy it's rude. 💅

🧚 scenario three: you want to align LOTS of sequences 🧚

suppose you want to align lots of sequences. you can construct a manageably small structural alignment of a representative set of sequences, build a CM with cmbuild, and then use the cmalign program to align any number of sequences to that CM. any number. go feral. 🌈

👑 the auxiliary tools 👑

Infernal also includes some auxiliary tools for working with large CM databases:

• cmfetch fetches one or more CMs from a database;
• cmstat prints summary statistics about a CM file.

and for compatibility with previous versions of Infernal, as well as with HMMER, the cmconvert program converts CM files to a few other formats. legacy support, we love her. 🫶

lastly, the cmemit program generates (simulates) "homologous" sequences by sampling from a CM. it can also generate a "consensus" sequence. cute little sequence generator, no notes. 🎀

⭐ every single one of these programs has its own man page, bestie. this one is just the overview.

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🌟 SEE ALSO 🌟

This is a summary man page for the entire Infernal package. See individual man pages — cmbuild(1), for example — for usage, options, and description of each program in the package. iykyk, go read the one you actually need. 📖

For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page (http://eddylab.org/infernal/).

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💜 COPYRIGHT 💜

Copyright (C) 2023 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. open source besties rise up 🫶

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

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✨ AUTHOR ✨

http://eddylab.org

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and that's the page!! 💖 this was Infernal 1.1.5, from Sep 2023, written up in the Infernal Manual — so if you ever need to cite it or summon it or whatever, that's the version, that's the date, slay, bye bestie 🌸🦋✨