PROPHECY(1e)

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

💖 PROPHECY(1e) — the EMBOSS Manual for Debian girlies 💖

okay so bestie, sit down, hydrate, because we're talking about prophecy, section 1e of the manual, and she is that girl. ✨

✨ NAME ✨

prophecy — Create frequency matrix or profile from a multiple alignment

like. she literally builds you a frequency matrix OR a profile out of a multiple alignment. main character behaviour fr fr 👑

🎀 SYNOPSIS 🎀

prophecy -sequence seqset -type list -datafile matrixf -name string
         -threshold integer -open float -extension float
         -outfile outfile

prophecy -help

and yes, prophecy -help is right there when you need her 🫶

🌸 DESCRIPTION 🌸

so prophecy is a command line program from EMBOSS — and if you don't know, EMBOSS is literally "the European Molecular Biology Open Software Suite" 💅 no cap.

she belongs to the "Nucleic:Profiles,Protein:Profiles" command group(s). so like, she runs with the profile girlies. that's her vibe. that's her era. 🦋

💅 OPTIONS 💅

🌈 Input section 🌈

  • -sequence seqset — your sequence set goes here, bestie. that's the input, periodt.
  • -type list — picks the type. Default value: F
  • -datafile matrixf — the data file. Default value: @($(type) = G: Epprofile H: EBLOSUM62 F: EBLOSUM62) — yes that's the whole conditional-looking thing, she's fancy like that 💀

⭐ Required section ⭐

  • -name string — the name. Default value: mymatrix

like it's required but she still has a default, iconic behaviour honestly.

🔥 Profile type specific options 🔥

  • -threshold integer — Default value: 75

🧚 Gap options 🧚

  • -open float — the gap open penalty. Default value: 3.0
  • -extension float — the gap extension penalty. Default value: 0.3

gaps in the alignment? handled. we love a girl who plans ahead. 💖

💜 Output section 💜

  • -outfile outfile — where it all goes. your output file, your moment. ✨

💀 BUGS 💀

found a bug?? not her fault but okay, report it bestie:

👑 SEE ALSO 👑

prophecy is fully documented via the tfm(1) system. so if you want the full lore, that's where the lore lives. iykyk 📚

🫶 AUTHOR 🫶

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

  • Wrote the script used to autogenerate this manual page.

the autogenerated-manpage pipeline ate and left no crumbs, 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.

ok so real talk: this page was autogenerated, so don't come for the vibes, come for the facts. 💖

and that's the whole thing, bestie!! this manual page came to you from EMBOSS 6.4.0, dated 05/11/2012, and it's the PROPHECY(1e) page of the EMBOSS Manual for Debian. slay, go profile something. 💅✨🎀🦋

📦 where this page comes from