COVES-SE(1)

✨ NAME ✨

okay bestie, meet coves-SE — she's the one who does detection of transfer RNA genes in genomic sequence. that's it, that's the whole job. tRNA hunting, no cap 🧬✨

🎀 DESCRIPTION 🎀

so like, the vibe is this: coves-SE is a user command (hi, that's what the manual name means, User Commands energy 💅) and it wants you to talk to it in a very specific way or it will simply not.

if you get it wrong, it hits you with:

FATAL: Usage: coves [-options] <CM file> <seqfile> where options are:

yep. FATAL. all caps. it's giving dramatic 💀. and look at the usage line — you hand over a CM file and a seqfile, in that order, and then whatever options you want. no cap, that's the whole deal.

and the options are... literally these:

• -a — show all pairs, not just Watson-Crick ones. lowkey more is more, bestie 🫶
• -g <gcfrac> — set the expected background GC composition. the default is 0.5, so if you don't say anything she assumes an even split 🌗
• -m — mountain representation of the structural alignment 🏔️ iconic, honestly
• -s — secondary structure string representation of the structural alignment 🪜✨

heads up bestie: that last one got cut short in the source — it says "secondary structure string representation of" and then just trails off into the structural alignment. we're keeping it exactly as it is, no inventing, no guessing 🎀

💖 AUTHOR 💖

this manpage was written by Nilesh Patra for the Debian distribution, and — slay — it can be used for any other usage of the program too. sharing is caring fr fr 🌈

that's the whole page, bestie, you ate it 🍓. this was coves-SE version 2.0.9+ds, dated July 2021 — mwah, go hunt some tRNA genes 💜👑🦋