GLAM2-PURGE(1)

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

🎀 GLAM2-PURGE(1) — the glam2 Manual's chaotic little sister 🎀

okay bestie, buckle up, we're doing the glam2 Manual thing and this one is specifically about glam2-purge(1). yes it's a whole section 1 man page, yes it lives in the glam2 Manual, no you don't need to be scared 💖

✨ NAME ✨

glam2-purge — the little icon that removes redundant sequences from a FASTA file 🧹✨

🌸 SYNOPSIS 🌸

glam2-purge file score [options]

like. that's it. a file, a score, and then whatever options your heart desires 💅

🦋 DESCRIPTION 🦋

so glam2-purge is a modified version of Andrew Neuwald's purge program, and its whole job is removing redundant sequences from a FASTA file. and no, this isn't just busywork — it's recommended, because highly similar sequences would otherwise distort the search for motifs. and we do NOT let the search get distorted. not on our watch 🙈

Purge works with either DNA or protein sequences, and it creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. the threshold is literally the score you hand it. you're the threshold-setter. main character energy fr fr 👑

the output file gets named:

<file>.<score>

okay and the scoring? the alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. (yes, proteins and DNA get different little scoring situations. slay.)

and plot twist — Purge can also be used to mask tandem repeats. it uses the XNU program for this purpose 🧚

💅 OPTIONS 💅

  • -n — Sequences are DNA (default: protein).
  • -b — Use blast heuristic method (default for protein).
  • -e — Use an exhaustive method (default for DNA).
  • -q — Keep first sequence in the set.
  • -x — Use xnu to mask protein tandem repeats.

periodt. five options, all accounted for, no stragglers 💖

🌈 SEE ALSO 🌈

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, it's giving ✨informed✨

📚 REFERENCES 📚

Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618–1632, 1995. Please cite it if you use Purge. (academic besties stay citable, that's the rule 🫶)

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 👑

  • Andrew Neuwald
    • Author of purge, renamed glam2-purge in Debian.
  • Martin Frith
    • Modified purge to be ANSI standard C and improved the user interface.
  • Timothy Bailey
    • Modified purge to be ANSI standard C and improved the user interface.
  • Charles Plessy <plessy@debian.org>
    • Formatted this manpage in DocBook XML for the Debian distribution.

The source code and the documentation of Purge and GLAM2 are released in the public domain. no cap, it's free, it's yours, go wild 🌈

💌 cute little sign-off: this page is from GLAM2 1056, dated 05/19/2008, and it's filed under GLAM2-PURGE(1). bye bestie, go purge some redundant sequences, you're gonna ate 💅🎀✨
📦 where this page comes from