OLIGOTM(1)

💖 OLIGOTM 💖

okay bestie, welcome to the oligotm page from the Primer3 User Manuals — yes it's a real Unix manual page, no it's not boring, stay with me 🫶

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✨ NAME ✨

oligotm — prints oligo's melting temperature on stdout 🌡️✨

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🎀 SYNOPSIS 🎀

oligotm [OPTIONS] {oligo}

where oligo is a DNA sequence of between 2 and 36 bases 🧬

heads up: 2 to 36 bases. not 1. not 37. the vibes have limits 💅

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🦋 DESCRIPTION 🦋

oligotm prints the melting temperature of a given deoxyribonucleotide on the standard output. It is part of the oligotm library. that's it, that's the whole job, and honestly? it eats 💅

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🌸 OPTIONS 🌸

• -mv monovalent_conc — Concentration of monovalent cations in mM, by default 50 mM. 💜
• -dv divalent_conc — Concentration of divalent cations in mM, by default 0 mM. 💜
• -n dNTP_conc — Concentration of deoxynucleotide triphosphate in mM, by default 0 mM. 💜
• -d dna_conc — Concentration of DNA strands in nM, by default 50 nM. 💜
• -tp [0|1] — Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
  • 0 — Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but not the recommended value. 🙈
  • 1 — Use nearest neighbor parameter from SantaLucia 1998. This is the recommended value. 👑
• -sc [0..2] — Specifies salt correction formula for the melting temperature calculation:
  • 0 — Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but not the recommended value. 🙈
  • 1 — SantaLucia 1998. This is the recommended value. 👑
  • 2 — Owczarzy et al., 2004. 🌈
• -i — prints references to publications which were used for thermodynamic calculations. 📚✨

not me pointing out that -tp 0 and -sc 0 are the defaults but not the recommended values 😭 the iconique old-school behaviour is still just sitting there as the default, that's literally canon, don't @ me

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📖 REFERENCE 📖

Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386. 🫶

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👀 SEE ALSO 👀

primer3_core(1) ntdpal(1)

go read those too bestie, they're giving main character energy ⭐

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💀 COPYRIGHT 💀

Copyright © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky

All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of oligotm. 📄

This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself. 💜

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and that's the whole page, bestie 🎀 this was oligotm 1.1.4, dated 11/30/2011 — an absolute legend, no cap, slay, periodt ✨💅🦋