PEPDIGEST(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 PEPDIGEST(1e) 💖

okay bestie, gather round, because this is pepd digest from the EMBOSS Manual for Debian and it's literally about telling you where your protein gets chopped up by proteolytic enzymes or reagents. it's giving ✂️ protein gossip ✂️ and honestly? obsessed.

✨ NAME ✨

pepd digest — reports on protein proteolytic enzyme or reagent cleavage sites 🧬💅

🌸 SYNOPSIS 🌸

pepd digest -seqall seqall -mwdata datafile -menu list -mono boolean
          -unfavoured boolean -ragging boolean -termini list
          -overlap boolean -allpartials boolean -outfile report

pepd digest -help

🦋 DESCRIPTION 🦋

so pepd digest is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). no cap, that's the whole acronym. it's part of the "Protein:Composition" command group(s), so if you're out here vibing with protein composition tools, this is your girl. 💖

👑 OPTIONS 👑

🎀 Input section

  • -seqall seqall — hand over your sequences, bestie. all of them. 💖
  • -mwdata datafile — molecular weight data for amino acids. Default value: Emolwt.dat ⭐

🌈 Required section

  • -menu list — Default value: 1
  • -mono boolean — Default value: N

💜 Advanced section

  • -unfavoured boolean — okay so this one is a whole essay, and it matters, so let's go 🫶

Trypsin will not normally cut after 'KR' if they are followed by any of 'KRIFLP'.

Lys-C will not normally cut after 'K' if it is followed by 'P'.

Arg-C will not normally cut after 'R' if it is followed by 'P'.

V8-bicarb will not normally cut after 'E' if it is followed by any of 'KREP'.

V8-phosph will not normally cut after 'DE' if they are followed by 'P'.

Chymotrypsin will not normally cut after 'FYWLM' if they are followed by 'P'.

Specifying unfavoured shows these unfavoured cuts as well as the favoured ones. so you get the whole chaotic picture, not just the well-behaved cuts. 💀

  • -ragging boolean — allows semi-specific and non-specific digestion. this option is particularly useful for generating lists of peptide sequences for protein identification using mass-spectrometry. iykyk 🔥
  • -termini list — Default value: 1

🍓 Output section

  • -overlap boolean — used for partial digestion. shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it. literally one, not two, do not come for her. 💅
  • -allpartials boolean — as for overlap but fragments containing more than one potential cut site are included. she said go big or go home ✨
  • -outfile report — where the report goes, bestie 📝

💀 BUGS 💀

found a bug? not cute, but okay. bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). they'll fix it, periodt. 🫶

🌟 SEE ALSO 🌟

pepd digest is fully documented via the tfm(1) system. go read that too, bestie, she's thorough. 📚

💖 AUTHOR 💖

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. iconic behaviour, honestly. 👑

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

EMBOSS 6.4.0 · 05/11/2012 · PEPDIGEST(1e)

and that's the whole page, bestie 💜 this was autogenerated energy from back in the day, and now you know every single flag. go digest some proteins, you absolute main character 🦋✨

📦 where this page comes from