DIGEST(1e)

💖 DIGEST(1e) — the EMBOSS glow-up 💖

okay bestie, listen up — this is the manual page for digest, from the EMBOSS Manual for Debian (EMBOSS = the European Molecular Biology Open Software Suite, iykyk). It's giving "Protein:Motifs" command group energy. 🧬✨

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✨ NAME ✨

digest — reports on protein proteolytic enzyme or reagent cleavage sites 🦋

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🎀 SYNOPSIS 🎀

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

digest -help

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🌸 DESCRIPTION 🌸

digest is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). No cap. It's part of the "Protein:Motifs" command group(s). 💅

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💅 OPTIONS 💅

🌈 Input section 🌈

• -seqall seqall — the sequence input, bestie. That's the whole vibe here.
• -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 this one is lowkey the whole lore, so sit with me:
  • 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 polite version. 😭✨

• -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. it's giving lab main character energy 🔬🔥
• -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. no cap, that's the rule. 🌟
• -allpartials boolean — as for overlap but fragments containing more than one potential cut site are included. the inclusive queen 👑
• -outfile report — where the report goes, bestie. 📝

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💀 BUGS 💀

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). Found a bug? go tell them, don't be shy 🐛🙈

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🦋 SEE ALSO 🦋

digest is fully documented via the tfm(1) system. go read that one too, iykyk 📚✨

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💖 AUTHOR 💖

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

• wrote the script used to autogenerate this manual page. iconic behaviour honestly 🎀

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🌸 COPYRIGHT 🌸

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. 🫶

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and that's the whole page bestie — this was EMBOSS 6.4.0, dated 05/11/2012, and the page itself is DIGEST(1e). slay, go digest some proteins 💅🧬✨