GLAM2SCAN(1)

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

💖 GLAM2SCAN(1) 💖

okay bestie, welcome to the glam2 Manual — this is the page for glam2scan, and yes it's giving iconic. sit down, hydrate, let's go 🫶

✨ NAME ✨

glam2scan — finds a GLAM2 motif in a database 🔍💅

🌸 SYNOPSIS 🌸

glam2scan [options] alphabet my_motif.glam2 my_seqs.fa

An alphabet other than p or n is interpreted as the name of an alphabet file. not me getting a whole file dropped in as an alphabet 😭 but that's literally how it works.

🦋 DESCRIPTION 🦋

glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits the motif. score = how much it ate, how much it left on the plate 🍓

✨ OPTIONS (DEFAULT SETTINGS) ✨

lowkey the defaults are already in the parentheses for you, so you don't even gotta guess 👑

  • -h — Show all options and their default settings. the "tell me everything" button, we love her
  • -o — Output file (stdout). default is stdout, aka screaming into the void, but make it useful
  • -n — Number of alignments to report (25). twenty-five of them, periodt
  • -2 — Examine both strands — forward and reverse complement. both directions?? main character energy fr fr 🧚
  • -D — Deletion pseudocount (0.1).
  • -E — No-deletion pseudocount (2.0).
  • -I — Insertion pseudocount (0.02).
  • -J — No-insertion pseudocount (1.0).
  • -d — Dirichlet mixture file. a whole file for the mixture, she's fancy
ngl bestie, those pseudocounts are doing the quiet heavy lifting. don't just yolo-change them, okay? 🙈

🌈 SEE ALSO 🌈

The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. go read it, iykyk 📚✨

📖 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).

bestie. cite the paper. it's the bare minimum and it's free 💖

👑 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. formatting queen 🎀

The source code and the documentation of GLAM2 are released in the public domain. public domain!! no cap, take it and go slay 🌈

and that's the whole page, bestie 🫶 this was GLAM2 1056, dated 05/19/2008 — yes she's vintage, and yes she still ate 💅✨ bye!!

📦 where this page comes from