GLAM2FORMAT(1)

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

💖 GLAM2FORMAT(1) 💖

okay bestie, welcome to the glam2 Manual — this one's called glam2format and it's literally the glow-up artist for your motifs. no cap. ✨

🌸 NAME 🌸

glam2format — converts GLAM2 motifs to FASTA or MSF format 🦋

✨ SYNOPSIS ✨

glam2format [options] my_format my_motif.glam2

Formats: fasta, msf.

💅 DESCRIPTION 💅

so basically glam2format reads in a motif that glam2 found, and writes it back out in a standard alignment format — that's FASTA-with-gaps or MSF, your pick. why do we care? because this lets you pass that alignment to third-party software, including the graphical visualization girlies like Kalignvu, Boxshade, and WebLogo. main character collab fr. 🫶

but — and this is the part where we keep it real — not all the motif information is preserved. in particular, the key positions are lost. 💀

also: only the top motif in glam2 output gets converted. just the one. periodt.

👑 OPTIONS (DEFAULT SETTINGS) 👑

  • -o — Output file (stdout). that's the default btw, it just vibes straight to your terminal unless you say otherwise.
  • -c — Make a compact alignment. here's the tea: by default, residues that are inserted between key positions are written as unaligned with each other. that best reflects glam2's intention, but ngl it can make the alignment large and absolutely full of gaps. 😭 with -c, inserted residues are written as arbitrarily aligned with each other, just as they appear in the glam2 output. shorter, messier, iconic.
  • -f — Sequence file to make a "global" alignment by adding flanking sequences from the original FASTA-format sequence file. the flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. also!! the sequences should have unique names and their order should be unchanged. don't shuffle them bestie i'm begging 🙈

🌈 SEE ALSO 🌈

boxshade(1), glam2(1), glam2mask(1), glam2-purge(1), glam2scan(1)

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).

🎀 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 real estate, as they say. 🧚

and that's the whole page bestie, go format some motifs 💖✨

mwah 💋 — this was GLAM2 version 1056, dated 05/19/2008. thanks for reading, ily, bye!! 🦋🌸💅

📦 where this page comes from