1 Name

MELTING - nearest-neighbor computation of nucleic acid hybridation

2 Synopsis

melting [options ]

3 Description

MELTING computes, for a nucleic acid duplex, the enthalpy and the entropy of the helix-coil transition, and then its melting temperature. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program uses the method of nearest-neighbors. The set of thermodynamic parameters can be easely changed, for instance following an experimental breakthrough. Melting is a free program in both sense of the term. It comes with no cost and it is open-source. In addition it is coded in ISO C and can be compiled on any operating system. Some perl scripts are provided to show how melting can be used as a block to construct more ambitious programs.

If you use MELTING, please quote

Le Novère. MELTING, a free tool to compute the melting temperature of nucleic acid duplex. Bioinformatics, 17: 1226-1227.

4 Options

The options are treated sequentially. If there is a conflict between the value of two options, the latter normally erases the former.

-Afile.nn

Informs the program to use file.nn as an alternative set of nearest-neighbor parameters, rather than the default for the specified hybridisation type (option -H). The standard distribution of melting provides some files ready-to-use: all97a.nn (Allawi et al 1997), bre86a.nn (Breslauer et al 1986), san96a.nn (SantaLucia et al 1996), sug96a.nn (Sugimoto et al 1996), san04a.nn (Santalucia et al 2004) (DNA/DNA), fre86a.nn (Freier et al 1986), xia98a.nn (Xia et al 1998) (RNA/RNA) and sug95a.nn (Sugimoto et al 1995) (DNA/RNA). The program will look for the file in a directory specified during the installation. However, if an environment variable NN_PATH is defined, melting will search in this one first. Be careful, the option -A changes the default parameter set defined by the option -H.

-Ccomplementary_sequence

Enters the complementary sequence, from 3' to 5'. This option is mandatory if there are mismatches between the two strands. If it is not used, the program will compute it as the complement of the sequence entered with the option -S

-Ddnadnade.nn

Informs the program to use the file dnadnade.nn to compute the contribution of dangling ends to the thermodynamic of helix-coil transition. The dangling ends are not taken into account by the approximative mode.

-Ffactor

This is the a correction factor used to modulate the effect of the nucleic acid concentration in the computation of the melting temperature. See section ALGORITHM for details.

-Gx.xxe-xx

Magnesium concentration (No maximum concentration for the moment). The effect of ions on thermodynamic stability of nucleic acid duplexes is complex, and the correcting functions are at best rough approximations.The published Tm correction formula for divalent Mg²⁺ ions of Owczarzy et al.(2008) can take in account the competitive binding of monovalent and divalent ions on DNA. However this formula is only for DNA duplexes.

-h

Displays a short help and quit with EXIT_SUCCESS.

-Hhybridisation_type

Specifies the hybridisation type. This will set the nearest-neighbor set to use if no alternative set is provided by the option -A (remember the options are read sequentially). Moreover this parameter determines the equation to use if the sequence length exceeds the limit of application of the nearest-neighbor approach (arbitrarily set up by the author). Possible values are dnadna, dnarna and rnadna (synonymous), and rnarna. For reasons of compatibility the values of the previous versions of melting A,B,C,F,R,S,T,U,W are still available although strongly deprecated. Use the option -A to require an alternative set of thermodynamic parameters. Important: If the duplex is a DNA/RNA heteroduplex, the sequence of the DNA strand has to be entered with the option -S

-Iinput_file

Provides the name of an input file containing the parameters of the run. The input has to contain one parameter per line, formatted as in the command line. The order is not important, as well as blank lines. example:

 -Hdnadna  
 -Asug96a.nn
 -SAGCTCGACTC
 -CTCGAGGTGAG
 -N0.2
 -P0.0001 
 -v 
 -Ksan96a

-ifile.nn

Informs the program to use file.nn as an alternative set of inosine pair parameters, rather than the default for the specified hybridisation type. The standard distribution of melting provides some files ready-to-use: san05a.nn (Santalucia et al 2005) for deoxyinosine in DNA duplexes, bre07a.nn (Brent M Znosko et al 2007)for inosine in RNA duplexes. Note that not all the inosine mismatched wobble's pairs have been investigated. Therefore it could be impossible to compute the Tm of a duplex with inosine pairs. Moreover, those inosine pairs are not taken into account by the approximative mode.

-Ksalt_correction

Permits to chose another correction for the concentration in sodium. Currently, one can chose between wet91a, san96a, san98a. See section ALGORITHM

-kx.xxe-xx

Potassium concentration (No maximum concentration for the moment). The effect of ions on thermodynamic stability of nucleic acid duplexes is complex, and the correcting functions are at best rough approximations.The published Tm correction formula for sodium ions of Owczarzy et al.(2008) is therefore also applicable to buffers containing Tris or KCl. Monovalent K⁺, Na⁺, Tris⁺ ions stabilize DNA duplexes with similar potency, and their effects on duplex stability are additive. However this formula is only for DNA duplexes.

-L

Prints the legal informations and quit with EXIT_SUCCESS.

-Mdnadnamm.nn

Informs the program to use the file dnadnamm.nn to compute the contribution of mismatches to the thermodynamic of helix-coil transition. Note that not all the mismatched Crick's pairs have been investigated. Therefore it could be impossible to compute the Tm of a mismatched duplex. Moreover, those mismatches are not taken into account by the approximative mode.

-Nx.xxe-xx

Sodium concentration (between 0 and 10 M). The effect of ions on thermodynamic stability of nucleic acid duplexes is complex, and the correcting functions are at best rough approximations. Moreover, they are generally reliable only for [Na⁺] belonging to [0.1,1 M]. If there are no other ions in solution, we can use only the sodium correction. In the other case, we use the Owczarzy's algorithm.

-Ooutput_file

The output is directed to this file instead of the standard output. The name of the file output_file

The