GLAM2(1)

📦 version 1064, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ GLAM2(1) ✨ — the glam2 manual page, bestie edition 💖

okay so this is the page for glam2 from the glam2 Manual, and I'm gonna walk you through literally every single thing on it. no skips. no "you'll figure it out." we're doing this together 🫶

🌸 NAME 🌸

glam2 — Gapped Local Alignment of Motifs. that's the whole name. iconic. short. slays.

🎀 SYNOPSIS 🎀

glam2 [options] alphabet my_seqs.fa

and listen, this next part matters:

An alphabet other than p or n is interpreted as the name of an alphabet file. so like, p and n are the special ones, and anything else is a filename, periodt.

🦋 DESCRIPTION 🦋

GLAM2 is a software package for finding motifs in sequences, and those sequences are typically amino-acid or nucleotide sequences. ngl that's its whole thing.

so what's a motif? a motif is a re-occurring sequence pattern 💫 — the classic examples are the TATA box and the CAAX prenylation motif. yes bestie, real ones.

and here's the main innovation, the part that makes GLAM2 the main character: it allows insertions and deletions in motifs. like, gaps. it's giving flexible. it's giving gapped local alignment. the name was not lying to you 💅

👑 OPTIONS (DEFAULT SETTINGS) 👑

this is the big one. every flag, every default, all of it. buckle up 🎀

  • -h — Show all options and their default settings. (the "wait what were the defaults again" button)
  • -o — Output file (default: stdout). so if you don't say anything, it just yells into your terminal 📢
  • -r — Number of alignment runs (default 10).
  • -n — End each run after this many iterations without improvement (default 10000).
  • -2 — Examine both strands — forward and reverse complement. double the strands, double the slay ✨
  • -z — Minimum number of sequences in the alignment (default 2).
  • -a — Minimum number of aligned columns (default 2).
  • -b — Maximum number of aligned columns (default 50).
  • -w — Initial number of aligned columns (default 20).
  • -d — Dirichlet mixture file.
  • -D — Deletion pseudocount (default 0.1).
  • -E — No-deletion pseudocount (default 2.0).
  • -I — Insertion pseudocount (default 0.02).
  • -J — No-insertion pseudocount (default 1.0).
  • -q — Weight for generic versus sequence-set-specific residue abundances (default 1e+99). that exponent is not a typo bestie, that's what it says.
  • -t — Initial temperature (default 1.2). 🔥
  • -c — Cooling factor per n iterations (default 1.44).
  • -u — Temperature lower bound (default 0.1).
  • -p — Print progress information at each iteration. (turn this on if you're nosy like me 🙈)
  • -m — Column-sampling moves per site-sampling move (default 1.0).
  • -x — Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (default 0).
  • -s — Seed for pseudo-random numbers (default 1).

💜 SEE ALSO 💜

go read these next, bestie, they're the friend group:

The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.

⭐ REFERENCE ⭐

If you use GLAM2, please cite:

MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).

cite the girls when you use their work, it's the rules 🫶

🌈 AUTHORS 🌈

  • Martin Frith — Author of GLAM2.
  • Timothy Bailey — Author of GLAM2.
  • Charles Plessy <plessy@debian.org> — Formatted this manpage in DocBook XML for the Debian distribution.

The source code and the documentation of GLAM2 are released in the public domain. free free free, no strings, iconic behaviour ✨

okay and that's the whole page!! mwah 💅 this was GLAM2 version 1056, dated 05/19/2008 — go find a motif, bestie, you got this 🦋🌸💖

📦 where this page comes from