PLOTORF(1e)

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

💖 PLOTORF(1e) 💖

okay bestie, gather round, we're doing a plotorf deep dive and it's in the EMBOSS manual for Debian, section 1e, so you know it's a command-line girly 🎀

✨ NAME ✨

plotorf — plot potential open reading frames in a nucleotide sequence

like... it literally draws you a picture of where the ORFs could be. iconic behavior. 🔥

🌸 SYNOPSIS 🌸

plotorf -sequence sequence -start string -stop string -graph xygraph
plotorf -help

that's it, that's the whole vibe. two ways in: give it a sequence and it does the thing, or hit it with -help and it tells you about itself. self-aware queen. 💅

🦋 DESCRIPTION 🦋

okay so plotorf is a command line program from EMBOSS (that's "the European Molecular Biology Open Software Suite", no cap, that's the actual expansion 💖).

it lives in the command group(s) "Nucleic:Gene finding,Nucleic:Translation,Display" — so it's out here doing gene finding, translation, and display. multihyphenate. main character energy fr fr. ✨

🎀 OPTIONS 🎀

💜 Input section

  • -sequence sequence — hand over your sequence right here, bestie. this is the nucleotide sequence we're plotting ORFs on. 🧚

💜 Advanced section

  • -start string — the start codon string you want it to look for.
    • Default value: ATG
  • -stop string — the stop codon string(s) you want it to look for. yes you can list several, they're comma-separated.
    • Default value: TAA,TAG,TGA

💜 Output section

  • -graph xygraph — where the plot goes. this is your xygraph output, your little picture of potential ORFs. 🎨

💀 BUGS 💀

found a bug? not me manifesting that but okay 😭 — bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or you can go straight to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

they're literally asking you to snitch on the bugs. do it. 🫶

🌈 SEE ALSO 🌈

plotorf is fully documented via the tfm(1) system. so if you want the whole lore, that's where it's at. iykyk. 📚

👑 AUTHOR 👑

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

  • Wrote the script used to autogenerate this manual page.

so like, credit where credit is due, they built the machine that built this page. respect. 💖

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.

tl;dr: same terms as EMBOSS, keep it moving, stay legal bestie. 💅

and that's the whole page!! mwah 💋 — this little number is EMBOSS 6.4.0, dated 05/11/2012, and it's the PLOTORF(1e) page from the EMBOSS Manual for Debian. slay, go plot some open reading frames, you got this 🦋✨🎀

📦 where this page comes from