TRIMEST(1e)

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

💖 trimest — bestie edition 💖

okay so this is TRIMEST(1e), straight out of the EMBOSS Manual for Debian, and she's here to help you yeet poly-A tails off your nucleotide sequences. no cap. 🧬✨

✨ NAME ✨

trimest — Remove poly-A tails from nucleotide sequences 🎀

🌸 SYNOPSIS 🌸

trimest -sequence seqall [-minlength integer] [-mismatches integer]
        [-reverse boolean] [-tolower toggle] -fiveprime boolean
        -outseq seqoutall

trimest -help

🦋 DESCRIPTION 🦋

so trimest is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). literally what it says on the tin. she lives in the "Nucleic:Functional sites,Edit" command group(s), and she's obsessed with her job 💅

👑 OPTIONS 👑

💜 Input section

  • -sequence seqall — this is where you hand her your sequences, bestie. feed the girl. 🍓

🌈 Additional section

  • -minlength integer — the minimum length a poly-A (or poly-T) tail has to be before she'll even consider removing it. and here's the tea: if there are mismatches in the tail, there must be at least this length of poly-A tail before the mismatch for that mismatch to count as part of the tail. default value: 4 ⭐
  • -mismatches integer — if there are this number or fewer contiguous non-A bases in a poly-A tail, then — as long as there are -minlength A bases before them — they get considered part of the tail and removed. periodt. for example, the terminal 4 A's of GCAGAAAA would be removed with the default values of -minlength=4 and -mismatches=1 (there are not at least 4 A's before the last G, so only the A's after it are considered part of the tail). meanwhile the terminal 9 bases of GCAAAAGAAAA would be removed — there are at least -minlength A's preceding the last G, so it's part of the tail. default value: 1 🔥
  • -reverse boolean — when a poly-T region at the 5' end of the sequence gets found and removed, it's likely the sequence is in the reverse sense. this option flips the sequence to the forward sense when it's written out. if this option is not set, then the sense will not be changed, no thoughts head empty. default value: Y 🦋
  • -tolower toggle — the poly-A region can be "masked" by converting the sequence characters to lower-case, and some non-EMBOSS programs e.g. fasta can interpret this as a masked region 👀 the sequence is unchanged apart from the case change. and psst — you might like to make sure the whole sequence is in upper-case before masking the specified regions to lower-case by using the -supper sequence qualifier. default value: N 💅

🧚 Advanced section

  • -fiveprime boolean — if this is set true, then the 5' end of the sequence gets inspected for poly-T tails, and they'll be removed if they're longer than any 3' poly-A tails. if this is false, then the 5' end is simply ignored, she said not today. default value: Y 💖

🎀 Output section

  • -outseq seqoutall — where the glow-up results go. your freshly trimmed sequences, served. ✨

😭 BUGS 😭

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). please be nice, they're trying 🙈

🔍 SEE ALSO 🔍

trimest 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. iconic behaviour, 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. slay 🌈

and that's the whole vibe, bestie — this page is brought to you by EMBOSS 6.4.0, dated 05/11/2012, and yes she's still serving TRIMEST(1e) energy after all these years 💅✨🎀

📦 where this page comes from