PRIMERS(1e)

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

💖 PRIMERS(1e) 💖

okay so this is primers from the EMBOSS Manual for Debian — literally the cutest lil tool for picking PCR primers, and no I will not be normal about it 🧬✨

🌸 NAME 🌸

primers — a simple version of primer3 that picks PCR primers for you, bestie 💅

✨ SYNOPSIS ✨

primers -sequence seqall [-targetregion range] [-minsize integer]
        [-maxsize integer] [-maxdifftm float] [-explainflag boolean]
        [-numreturn integer] -outfile outfile

primers -help

🦋 DESCRIPTION 🦋

So primers is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite," and yes the name is giving very official. It's part of the "Nucleic:Primers" command group(s), so it's hanging out with its little primer-picking friends 🫶

🎀 OPTIONS 🎀

🌈 Input section

  • -sequence seqall — the sequence you wanna choose primers from. Important: it has to be presented 5' -> 3', no exceptions, the vibe check is strict here 💀

💜 Additional section

  • -targetregion range — if you specify one or more Targets then a legal primer pair has to flank at least one of them. A Target might be a simple sequence repeat site (like a CA repeat, cute) or a single-base-pair polymorphism. The value should be a space-separated list of <start>,<end> pairs, where <start> is the index of the first base of a Target, and <end> is the last. E.g. 50,51 requires primers to surround the 2 bases at positions 50 and 51 🎯
  • -minsize integer — the minimum acceptable length of a primer. Must be greater than 0 and less than or equal to MAX-SIZE. Default value: 18
  • -maxsize integer — the maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. This limit is governed by the maximum oligo size for which Primer3's melting-temperature is valid. Default value: 27
  • -maxdifftm float — the maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers. Default value: 100.0

🍓 Output section

  • -explainflag boolean — if this flag is non-0, produce LEFT-EXPLAIN and RIGHT-EXPLAIN output, which are intended to provide info on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons. Default value: N
  • -numreturn integer — the maximum number of primer pairs to return. The pairs that get returned are sorted by their 'quality' — in other words, by the value of the objective function (where a lower number indicates a better primer pair, periodt). Caution: setting this parameter to a large value will increase running time. Default value: 5
  • -outfile outfile — where the output goes, bestie 📁

😭 BUGS 😭

Found a bug? Not the vibe, but ok. 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) 🐛

👑 SEE ALSO 👑

primers 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. slay, 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 📜

and that's the whole page, bestie — this one's from EMBOSS 6.4.0, dated 05/11/2012, and it lives at PRIMERS(1e). go pick some primers, you absolute icon 💅✨🧬

📦 where this page comes from