SIRNA(1e)

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

💖 SIRNA(1e) 💖

okay bestie, welcome to the EMBOSS Manual for Debian page for sirna — yes, lowercase, yes, it's giving "little command, big job." sit down, hydrate, let's go 🫶

✨ NAME ✨

sirna — Finds siRNA duplexes in mRNA

🌸 SYNOPSIS 🌸

sirna -sequence seqall [-poliii boolean] [-aa boolean] [-tt boolean]
      [-polybase boolean] -outfile report -outseq seqoutall
      [-context boolean]

sirna -help

🦋 DESCRIPTION 🦋

so like, sirna is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). it's part of the "Nucleic:Functional sites,Nucleic:2D structure" command group(s). periodt 💅

👑 OPTIONS 👑

🎀 Input section

  • -sequence seqall — yeah that's it, that's the input. hand over your sequences, bestie.

🧚 Sequence input options

  • -poliii boolean — this one lets you select only the 21 base probes that start with a purine, so they can be expressed from Pol III expression vectors. it's the NARN(17)YNN pattern suggested by Tuschl et al. default value: N ✨
  • -aa boolean — select only those 23 base regions that start with AA. if you don't turn this on, then regions starting with AA just get favoured with a higher score — the ones that don't start with AA still get reported too. no gatekeeping, they're just not the favourites. default value: N 💖
  • -tt boolean — same vibe, other end: select only those 23 base regions that end with TT. leave it off and TT-enders just get a higher score as a lil treat, but non-TT regions are still reported. default value: N 🌸
  • -polybase boolean — if this is FALSE, then only those 23 base regions with no repeat of 4 or more of any bases in a row get reported. and heads up: no regions will ever be reported that have 4 or more G's in a row — that one's not optional, no cap. default value: Y 💀

🌈 Output section

  • -outfile report — the output is a table of the forward and reverse parts of the 21 base siRNA duplex. both the forward and reverse sequences are written 5' to 3', ready to be ordered. the last two bases have been replaced by 'dTdT'. the starting position of the 23 base region and the %GC content is also given. if you wish to see the complete 23 base sequence, then either look at the sequence in the other output file, or use the qualifier '-context' which will display the 23 bases of the forward sequence in this report with the first two bases in brackets. those first two bases do not form part of the siRNA probe to be ordered. iconic, honestly 🔥
  • -outseq seqoutall — this is a file of the sequences of the 23 base regions that the siRNAs are selected from. you may use it to do searches of mRNA databases (e.g. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on. very "trust but verify" of you 🧚
  • -context boolean — the output report file gives the sequences of the 21 base siRNA regions ready to be ordered. this does not give you an indication of the 2 bases before the 21 bases. it is often interesting to see which of the suggested possible probe regions have an 'AA' in front of them (i.e. it is useful to see which of the 23 base regions start with an 'AA'). this option displays the whole 23 bases of the region with the first two bases in brackets, e.g. '(AA)' to give you some context for the probe region.
YOU SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS WHEN YOU PLACE AN ORDER FOR THE PROBES. 🚨 like fr fr, do not. they're context only. default value: N

😭 BUGS 😭

bugs can be reported to the Debian Bug Tracking system (<http://bugs.debian.org/emboss>) — wait, no links, so: http://bugs.debian.org/emboss — or directly to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031. spill the tea, they want to know 🐛

💜 SEE ALSO 💜

sirna 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, script ✍️

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 thing, bestie — this page is from EMBOSS 6.4.0, dated 05/11/2012, and honestly? it ate. go find those duplexes. mwah 💅✨🦋

📦 where this page comes from