CHECKTRANS(1e)

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

💖 CHECKTRANS 💖

ok so this is the checktrans page from the EMBOSS Manual for Debian, and bestie, it's giving "tiny command, big opinions about STOP codons." it lives in section 1e, which is the EMBOSS manual, iykyk 🧬✨

✨ NAME ✨

checktrans — reports STOP codons and ORF statistics of a protein 🛑🔍

🌸 SYNOPSIS 🌸

checktrans -sequence seqall -orfml integer [-addlast boolean]
           -outfile outfile -outseq seqoutall -outfeat featout

checktrans -help

so like. you must hand it a sequence, an ORF minimum length, an outfile, an outseq and an outfeat. -addlast is the optional one, bestie, she's the flex option 💅

🦋 DESCRIPTION 🦋

checktrans is a command line program from EMBOSS, aka “the European Molecular Biology Open Software Suite” ✨. she is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s), which is honestly a whole vibe.

🎀 OPTIONS 🎀

💜 Input section

  • -sequence seqall — the sequence you're feeding her, no notes 🌸

🔥 Required section

  • -orfml integer — the minimum ORF length, periodt. Default value: 100

🌈 Additional section

  • -addlast boolean — okay so here's the lore: an asterisk in the protein sequence marks where a STOP codon is. checktrans just assumes every ORF ends in a STOP codon, like it's a whole rule. so if you force the sequence to end with an asterisk (only if there isn't one there already), checktrans will treat that end as a potential ORF. cute, right? 🫶 BUT — if an asterisk does get added, it is not counted in the reported STOP count. no inflation, we stay honest. Default value: Y

⭐ Output section

  • -outfile outfile — where the main output goes 📄
  • -outseq seqoutall — sequence file to hold output ORF sequences 🧬
  • -outfeat featout — file for output features 🎯

💀 BUGS 💀

found a bug? no gatekeeping 🙈 report it to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or slide directly into the EMBOSS developers' DMs at http://sourceforge.net/tracker/?group_id=93650&atid=605031.

👑 SEE ALSO 👑

checktrans is fully documented via the tfm(1) system. fr fr, that's where the real tea is 🍓

💅 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. 📜

lowkey a whole little legend, ngl — autogenerated and still serving looks. 🧚

ok and that's the whole page bestie, mwah 💖 EMBOSS 6.4.0, dated 05/11/2012, and this lil manual page is CHECKTRANS(1e) — go check those STOP codons, you got this 🫶🎀

📦 where this page comes from