NTTHAL(1)

💖 NTTHAL(1) 💖

okay bestie, welcome to the Primer3 User Manuals corner of the terminal 🫶 this is the glow-up guide for ntthal, and no cap, she's a whole vibe. let's get into it ✨

✨ NAME ✨

ntthal — she's the one who brings you Primer3's alignment functionality, built on the nearest-neighbor thermodynamical approach. iconic behaviour only 💅

🌸 DESCRIPTION 🌸

so ntthal is literally the sister of ntdpal, they're analogous fr fr 👯‍♀️

between two sequences, ntthal hunts down the alignment / sec structure that has the highest melting temperature 🔥 like she's picking the main character of the duplex situation.

and the way she does it? ntthal is based on the nearest-neighbor thermodynamical approach. periodt.

🎀 SYNOPSIS 🎀

ntthal OPTIONS oligo

💜 OPTIONS 💜

bestie there are a LOT of these and we're doing all of them, no skipping, we don't do that here 🙈

• -mv monovalent_conc — how much monovalent cations are in the mix, in mM. default is 50 mM 🧂
• -dv divalent_conc — the divalent cations concentration, in mM. default is 0 mM ✨
• -n dNTP_conc — concentration of deoxynycleotide triphosphate, in mM. default is 0 mM 🍓
• -d dna_conc — concentration of DNA strands, in nM. default is 50 nM 🧬
• -a mode — the alignment type, and your choices are END1, END2, ANY and HAIRPIN. default is ANY (when duplex) 💫
• -t temp — the temperature at which the duplex gets calculated. default is 37C 🌡️
• -r — this one makes the alignment NOT show up on stderr, and only Tm gets printed. quiet queen energy 🤫
• -maxloop size — the maximum size of secondary structures loops. default is 30 (and lowkey that's the maximum allowed length, currently) 🌀
• -path <path> — the path to the thermodynamic parameter files 📁
• -s1 DNA_oligomer — your first DNA oligomer 💖
• -s2 DNA_oligomer — and your second DNA oligomer 💖

heads up bestie: -maxloop's default of 30 is also the max allowed length right now, so don't go trying to be extra with it 💀

👑 AUTHORS 👑

this manual page was created by Andreas Tille <tille@debian.org> using help2man for Debian — but it can be freely used for any other purpose 🫶 generous king behaviour.

and that's the whole page, bestie!! this was version 2.3.6, dated December 2013 🌈 slay, bye 💅✨🦋