GARNIER(1e)

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

💅 GARNIER 💅

okay so bestie, welcome to the manual page for garnier — it's chilling in section 1e of the EMBOSS Manual for Debian, and it's literally here to hold your hand through protein secondary structure prediction. no cap.

✨ NAME ✨

garnier — Predicts protein secondary structure using GOR method 🦋

🌸 SYNOPSIS 🌸

garnier -sequence seqall -idc integer -outfile report

garnier -help

🎀 DESCRIPTION 🎀

garnier is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). she is part of the "Protein:2D Structure" command group(s). icon behavior fr fr.

✨ OPTIONS ✨

💖 Input section

  • -sequence seqall — your input sequence, bestie. drop it here.

🧚 Advanced section

  • -idc integer — okay so this one is giving lore. In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used. 💅

🫶 Output section

  • -outfile report — where the report goes. that's it, that's the vibe.

😭 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).

ngl if you find a bug, report it — the devs are the main characters of the fix-it arc.

👑 SEE ALSO 👑

garnier is fully documented via the tfm(1) system. iykyk.

💜 AUTHOR 💜

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

  • Wrote the script used to autogenerate this manual page.

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.

that's the whole page bestie, you ate it 🍓✨

this iconic little doc came to you courtesy of EMBOSS 6.4.0, dated 05/11/2012 — periodt, stan, and go predict some secondary structure 💅🎀

📦 where this page comes from