CPGPLOT(1e)

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

✨ CPGPLOT ✨

okay so bestie, welcome to cpgplot 💖 this is a page from the EMBOSS Manual for Debian, and it's all about finding and plotting CpG islands in nucleotide sequence(s) 🧬✨ no cap.

🌸 NAME 🌸

cpgplot — identify and plot CpG islands in nucleotide sequence(s) 🦋

🎀 SYNOPSIS 🎀


cpgplot -help

💅 DESCRIPTION 💅

So cpgplot is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite" 👑 — and it's part of the "Nucleic:CpG Islands" command group(s). it's giving bioinformatics main character energy fr fr 🧚

✨ OPTIONS ✨

🌈 Input section 🌈

  • -sequence seqall — bestie, this is where your sequence goes 🫶

💜 Required section 💜

  • -window integer — the percentage CG content and the Observed frequency of CG get calculated inside a window, and this parameter sets how big that window is. then the window slides down the sequence and those same statistics get recalculated at every position the window moves to. Default value: 100 ✨
  • -minlen integer — sets the minimum length a CpG island has to be before it gets reported, like a little height requirement at the club 💅 Default value: 200
  • -minoe float — sets the minimum average observed-to-expected ratio of C plus G to CpG, measured across a set of 10 windows, that's required before a CpG island gets reported. Default value: 0.6
  • -minpc float — sets the minimum average percentage of G plus C across a set of 10 windows that's required before a CpG island gets reported. Default value: 50.

🦋 Output section 🦋

  • -outfile outfile — sets the name of the file that holds the report: the input sequence name, the CpG island parameters, and the output details of any CpG islands that were found 📝✨
  • -plot toggle — Default value: Y
  • -graph xygraph — your graph output spot, iykyk 🎀
  • -obsexp boolean — if this is set to true, then the graph of the observed to expected ratio of C plus G to CpG within a window gets displayed. Default value: Y 🔥
  • -cg boolean — if this is set to true, then the graph of the regions that have been determined to be CpG islands gets displayed. Default value: Y 💖
  • -pc boolean — if this is set to true, then the graph of the percentage C plus G within a window gets displayed. Default value: Y 🌸
  • -outfeat featout — file for output features 👑

💀 BUGS 💀

found a bug? not the vibe, but okay 😭 you can report them to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or slide directly into the EMBOSS developers' DMs (http://sourceforge.net/tracker/?group_id=93650&atid=605031) 🫶

🌟 SEE ALSO 🌟

cpgplot is fully documented via the tfm(1) system. periodt 💅

👑 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. 📜

and that's the whole page bestie, every last flag accounted for, no skips, no cap 💖

okay so this was CPGPLOT(1e) from EMBOSS 6.4.0, dated 05/11/2012 — mwah, iconic, love that for us 🌈💜✨

📦 where this page comes from