MELTING(1)

📦 version 5.2.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ melting(1) — User Commands ✨

okay bestie, sit down, hydrate, and get comfy because today we're talking about MELTING 💖 — and no, it's not about ice cream melting in the sun (though relatable). this whole manual is about computing the melting temperature of a nucleic acid duplex, and honestly? iconic little chemistry moment. let's get into it 🧬🔥

🌸 NAME 🌸

melting — compute the melting temperature of nucleic acid duplex 🫶

📖 DESCRIPTION 📖

okay so if you want the deep lore, there's a whole user-guide waiting for you. just type man melting to pull it up, or go peek at one of the melting.xxx files — the xxx is standing in for ps (postscript), pdf or html. pick your format, bestie, they're all valid 💅

💅 OPTIONS 💅

here's the tea about MELTING 5:

  • -h — shows you this help and then dips. bye 👋
  • -L — shows the legal information and quits. the fine print era 📜
  • -V — prints the version number. identity check, who are you 💁‍♀️
  • -p — returns the path where the calorimetric tables live. lowkey a lil scavenger hunt 🗺️

🚨 Mandatory options

these ones are not optional, bestie. no skipping, no "i'll do it later," we're doing it now ✋💖

  • -S [sequence] — the nucleic acid sequence, mandatory. and the sense of this sequence has to be 5'-3'. don't fight it, that's just the rule 🧬
  • -C [complementary sequence] — the nucleic acid complementary sequence. this one's mandatory only if there are inosine bases or azobenznes in the sequence you entered with -S. the sense of this sequence has to be 3'-5''. yes, two apostrophes, that's literally how it's written, i don't make the rules 😭
  • -E [agent1=concentration1:agent2=concentration2] — sets the different agent concentrations in the solution. the agents can be cations (Na, K, Tris, Mg for Na+, K+, Tris+ and Mg2+), dNTP, or other agents (DMSO, formamide). concentrations are in Mol/L but there are exceptions: DMSO is a percentage, and formamide is a percentage if the method lincorr is chosen and in Mol/L if the method bla96 is chosen. at least one cation concentration is mandatory, everything else is optional. go read the documentation for the concentration limits — it depends on the correction you're using 👀
  • -P [nucleotide concentration] — concentration in mol/L of the nucleic acid strand in excess, mandatory. the star of the show, the one in excess 💅
  • -H [hybridization] — the type of hybridization, mandatory. four types are allowed:
    • dnadna (DNA duplex)
    • rnarna (RNA duplex)
    • dnarna or rnadna (hybrid DNA/RNA)
    • mrnarna or rnamrna (2-o-methyl RNA/RNA)

the type of hybridization defines the kind of the sequence and its complementary.

Ex: dnarna = the sequence (entered with the option -S) is a DNA sequence and its complementary (entered with the option -C) is a RNA sequence.

Ex: rnadna = the sequence (entered with the option -S) is a RNA sequence and its complementary (entered with the option -C) is a DNA sequence 🌈

✨ General options

  • -v — switches ON the verbose mode, issuing a lot more info. default is OFF. turn it on if you want the full commentary track 🎙️
  • -T [threshold value] — the threshold for approximative computation. default is 60 ⭐
  • -nnpath [folder pathway] — changes the default pathway (Data) where the default calorimetric tables (thermodynamic parameters) are found. relocating the vibes 📁
  • -O [filename] — writes the results into an output file. filename is the name or the pathway of the file. save it, don't lose it 🎀
  • -self — to precise that the sequence entered with the option -S is self complementary. no complementary sequence is mandatory. the program automatically can detect a self complementary sequence for perfect matching sequences or sequences with dangling ends — in those cases, the option -self is not necessary. otherwise we need to precise that the sequences are self complementary. it's giving "i know myself" energy 🪞
  • -F [factor value] — correction for the concentration of nucleic acid. F is automatically 1 if the sequences are self complementary. otherwise F is 4 if the both strands are present in equivalent amount and 1 if one strand is in excess. the default factor value is 4 💜

🔬 Set of thermodynamic parameters and methods 🔬

by default, the approximative mode is used for oligonucleotides longer than 60 bases (the default threshold value), otherwise the nearest neighbor model is used. so the vibes pick themselves, cute ✨

  • -am [optional name] — forces to use a specific approximative formula. you can use one of the following:
    • (DNA)
      • ahs01 (from von Ahsen et al. 2001)
      • che93 (from Marmur 1962, Chester et al. 1993)
      • che93corr (from von Ahsen et al. 2001, Marmur 1962, Chester et al. 1993)
      • schdot (Marmur-Schildkraut-Doty formula)
      • owe69 (from Owen et al. 1969)
      • san98 (from Santalucia et al. 1998)
      • wetdna91 (from Wetmur 1991) (by default)
    • (RNA)
      • wetrna91 (from Wetmur 1991) (by default)
    • (DNA/RNA)
      • wetdnarna91 (from Wetmur 1991) (by default)

if there is no formula name after the option -am, we will compute the melting temperature with the default approximative formula 🧮

  • -nn [optional name] — forces to use a specific nearest neighbor model. you can use one of the following:
    • (DNA)
      • all97 (from Allawi and Santalucia 1997) (by default)
      • bre86 (from Breslauer et al. 1986)
      • san04 (from Hicks and Santalucia 2004)
      • san96 (from Santalucia et al. 1996)
      • sug96 (from Sugimoto et al 1996)
      • tan04 (from Tanaka et al. 2004)
    • (RNA)
      • fre86 (from Freier al. 1986)
      • xia98 (from Xia et al. 1998) (by default)
    • (DNA/RNA)
      • sug95 (from Sugimoto et al. 1995) (by default)
    • (mRNA/RNA)
      • tur06 (from Kierzek et al. 2006) (by default)

if there is no formula name after the option -nn, we will compute the melting temperature with the default nearest neighbor model. each nearest neighbor model uses a specific xml file containing the thermodynamic values. if you want to use another file, write the file name or the file pathway preceded by : (-nn [optionalname:optionalfile]).

Ex: -nn tan04:fileName if you want to use the nearest neighbor model from Tanaka et al. 2004 with the thermodynamic parameters in the file fileName.

Ex: -nn :fileName if you want to use the default nearest neighbor model with the thermodynamic parameters in the file fileName 📂

  • -sinMM [name] — forces to use a specific nearest neighbor model for single mismatch(es) in the sequences. you can use one of the following:
    • (DNA)
      • allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
    • (DNA/RNA)
      • wat10 (from Watkins et al. 2011) (by default)
    • (RNA)
      • tur06 (from Lu et al. 2006)
      • zno07 (from Davis et al. 2007) (by default)
      • zno08 (from Davis et al. 2008)

to change the file containing the thermodynamic parameters for single mismatch computation, the same syntax as the one for the -nn option is used 💫

  • -GU [name] — forces to use a specific nearest neighbor model for GU base pairs in RNA sequences. you can use one of the following:
    • tur99 (from Turner et al. 1999)
    • ser12 (from Serra et al. 2012) (by default)

to change the file containing the thermodynamic parameters for GU base pairs computation, the same syntax as the one for the -nn option is used 🌸

  • -tanMM [name] — forces to use a specific nearest neighbor model for tandem mismatches in the sequences. you can use one of the following:
    • (DNA)
      • allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
    • (RNA)
      • tur99 (from Mathews et al. 1999) (by default)

to change the file containing the thermodynamic parameters for tandem mismatches computation, the same syntax as the one for the -nn option is used 🦋

  • -intLP [name] — forces to use a specific nearest neighbor model for internal loop in the sequences. you can use one of the following:
    • (DNA)
      • san04 (from Hicks and Santalucia 2004) (by default)
    • (RNA)
      • tur06 (from Lu et al. 2006) (by default)
      • zno07 (from Badhwarr et al. 2007, only for 1x2 loop)

to change the file containing the thermodynamic parameters for internal loop computation, the same syntax as the one for the -nn option is used 🌈

  • -sinDE [name] — forces to use a specific nearest neighbor model for single dangling end(s) in the sequences. you can use one of the following:
    • (DNA)
      • bom00 (from Bommarito et al. 2000) (by default)
      • sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
    • (RNA)
      • sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
      • ser08 (from Miller et al. 2008) (by default)

to change the file containing the thermodynamic parameters for single dangling end computation, the same syntax as the one for the -nn option is used ✨

  • -secDE [name] — forces to use a specific nearest neighbor model for second dangling end(s) in the sequences. you can use one of the following:
    • (DNA)
      • sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
    • (RNA)
      • sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
      • ser05 (from O'toole et al. 2005)
      • ser06 (from O'toole et al. 2006) (by default)

to change the file containing the thermodynamic parameters for second dangling end computation, the same syntax as the one for the -nn option is used 🎀

  • -lonDE [name] — forces to use a specific nearest neighbor model for long dangling end(s) in the sequences (self complementary sequences). you can use one of the following:
    • (DNA)
      • sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
    • (RNA)
      • sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)

to change the file containing the thermodynamic parameters for long dangling end computation, the same syntax as the one for the -nn option is used 👑

  • -sinBU [name] — forces to use a specific nearest neighbor model for single bulge loop(s) in the sequences. you can use one of the following:
    • (DNA)
      • san04 (from Hicks and Santalucia 2004)
      • tan04 (from Tanaka et al. 2004) (by default)
    • (RNA)
      • ser07 (from Blose et al. 2007)
      • tur06 (from Lu et al. 1999 and 2006) (by default)

to change the file containing the thermodynamic parameters for single bulge loop computation, the same syntax as the one for the -nn option is used 💖

  • -lonBU [name] — forces to use a specific nearest neighbor model for long bulge loop(s) in the sequences. you can use one of the following:
    • (DNA)
      • san04 (from Hicks and Santalucia 2004) (by default)
    • (RNA)
      • tur06 (from Mathews et al. 1999 and Lu et al 2006) (by default)

to change the file containing the thermodynamic parameters for long bulge loop computation, the same syntax as the one for the -nn option is used 🫶

  • -CNG [name] — okay bestie, this one got cut off mid-glow-up in the source, the plot continues in the next part, stay tuned 💅
  • the RNA CNG-repeat one (its flag name scrolled right off the top of this page, oops 😭) — forces a specific nearest neighbor model for RNA sequences made of CNG repeats (G(CNG)xC, where N is a single N/N mismatch). You get exactly one choice, bestie: bro05 (from Magdalena et al. 2005). Want to swap out the file with the thermodynamic parameters for RNA sequences composed of CNG repeats computation? Same syntax as the one for the -nn option. 💅
  • -ino [name] — forces a specific nearest neighbor model for the inosine base (I) in your sequences. Pick your fighter:
    • (DNA) san05 (from Watkins and Santalucia 2005) — this one's the default ✨
    • (RNA) zno07 (from Wright et al. 2007) — also the default ✨

Want to change the file with the thermodynamic parameters for inosine base computation? Same syntax as the one for the -nn option. 🎀

  • -ha [name] — forces a specific nearest neighbor model for the hydroxyadenine base (A*) in DNA sequences. One option and one option only: sug01 (from Kawakami et al. 2001). To change the file containing the thermodynamic parameters for hydroxyadenine base computation, same syntax as the one for the -nn option. 🦋
  • -azo [name] — forces a specific nearest neighbor model for DNA sequences containing azobenzene (cis : X_C or trans : X_T). Only asa05 (from Asanuma et al. 2005) is on the menu. To change the file containing the thermodynamic parameters for azobenzene computation, same syntax as the one for the -nn option. 🌸
  • -lck [name] — forces a specific nearest neighbor model for DNA sequences containing locked nucleic acid (Al, Tl, Cl or Gl). Your picks: mct04 (from McTigue et al. 2004) or owc11 (from Owczarzy et al. 2011, by default). To change the file containing the thermodynamic parameters for locked acid nucleic computation, same syntax as the one for the -nn option. 💖
  • -tanLck [name] — forces a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid (Al, Tl, Cl or Gl). Only owc11 (from Owczarzy et al. 2011, by default) — that's the whole roster. To change the file containing the thermodynamic parameters for locked acid nucleic computation, same syntax as the one for the -nn option. 🌈
  • -sinMMLck [name] — forces a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid with one single mismatch (Al, Tl, Cl or Gl). Only owc11 (from Owczarzy et al. 2011, by default) is available. To change the file containing the thermodynamic parameters for locked acid nucleic computation, same syntax as the one for the -nn option. 🧚

🌡️ Set of melting temperature corrections 🌡️

  • -ion [name] — forces a specific ion correction. Here's the whole lineup, no gatekeeping:

Sodium corrections:

  • (DNA) ahs01 (from von Ahsen et al. 2001), kam71 (from Frank-Kamenetskii et al 2001), owc1904 (equation 19 from Owczarzy et al. 2004), owc2004 (equation 20 from Owczarzy et al. 2004), owc2104 (equation 21 from Owczarzy et al. 2004), owc2204 (equation 21 from Owczarzy et al. 2004) (by default), san96 (from Santalucia et al. 1996), san04 (from Santalucia et al. 1998, 2004), schlif (from Schildkraut and Lifson 1965), tanna06 (from Tan et al. 2006), wetdna91 (from Wetmur 1991)
  • (RNA or 2-o methyl RNA) tanna07 (from Tan et al. 2007) (by default), wetrna91 (from Wetmur 1991)
  • (RNA/DNA) wetdnarna91 (from Wetmur 1991) (by default)

Magnesium corrections:

  • (DNA) owcmg08 (from Owczarzy et al. 2008) (by default), tanmg06 (from Tan et al. 2006)
  • (RNA or 2-o methyl RNA) tanmg07 (from Tan et al. 2007) (by default)

Mixed Na Mg corrections:

  • (DNA) owcmix08 (from Owczarzy et al. 2008) (by default), tanmix07 (from Tan et al. 2007)
  • (RNA or 2-o methyl RNA) tanmix07 (from Tan et al. 2007) (by default)

By default, the program uses the algorithm from Owczarzy et al 2008 : ratio = Mg^0.5 and monovalent = Na + Tris + K. 👑

  • if monovalent = 0, a magnesium correction is used.
  • if ratio < 0.22, a sodium correction is used.
  • if 0.22 <= ratio < 6, a mixed Na Mg correction is used.
  • if ratio >= 6, a magnesium correction is used.
  • -naeq [name] — forces a specific ion correction which gives a sodium equivalent concentration if other cations are present. Choose wisely:
    • (DNA) ahs01 (from von Ahsen et al 2001) (by default), mit96 (from Mitsuhashi et al. 1996), pey00 (from Peyret 2000)
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy. 💀
  • -DMSO [name] — forces a specific DMSO correction (DMSO is always in percent, just so you know). Your options:
    • (DNA) ahs01 (from von Ahsen et al 2001) (by default), mus81 (from Musielski et al. 1981), cul76 (from Cullen et al. 1976), esc80 (from Escara et al. 1980).
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy. 😭
  • -for [name] — forces a specific formamide correction. Two flavours, take your pick:
    • (DNA) bla96 (from Blake et al 1996) with formamide concentration in mol/L (by default), lincorr (linear correction) with a percent of formamide volume
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy. 🙈

✍️ AUTHOR ✍️

This manpage was written by Pranav Ballaney for the Debian distribution and can be used for any other usage of the program. 🫶

And that's a wrap, bestie!! 🎀 This whole thing is melting 5.2.0, dated June 2020, and it lives in section MELTING(1) — go forth and melt some duplexes, you absolute icon 💅✨🔥

📦 where this page comes from