MELTING Publisher's description
This program computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
This program computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program first computes the hybridisation enthalpy and entropy from the elementary parameters of each Crick's pair by the nearest-neighbor method. Then the melting temperature is computed. The set of thermodynamic parameters can be easely changed, for instance following an experimental breakthrough. MELTING is a free program (free as in freedom). Its source code is open, and you can get MELTING from here for free. MELTING 4 is written in ISO C and MELTING 5 in Java. It can be compiled on any operating system. Some perl scripts are provided for MELTING 4 to show how melting can be used as a block to construct more ambitious tools.
MELTING 5 has been rewritten from the beginning in Java (1.5) and provides a large set of thermodynamic models to compute the enthalpy and entropy of several structures in the duplex : perfectly matching sequences, single mismatch, tandem mismatch, internal loop, single dangling end, second dangling end, long dangling end (only one to four poly A), single bulge loop, long bulge loop, inosine base (I), hydroxyadenine (A*), azobenzene (cis X_C and trans X_T), locked nucleic acids (Al, Gl, Tl, Cl). MELTING 5 can manage a fourth type of hybridization : 2-o-methyl RNA/RNA. A lot of new ion corrections are available for Sodium, Magnesium, Potassium, Tris concentrations. The algorithm of Owczarzy et al is used to determine which correction to apply (see the MELTING 5 documentation for further information). New approximative formulas are available and to take into account the magnesium, tris and potassium concentrations, a sodium equivalent concentration is determined before computing the melting temperature with one of the approximative formulas. Some formulas are also available to correct the melting temperature when DMSO and formamide are present. The MELTING predictions accuracy has been improved in the 5 version, mostly for self complementary sequences.
System Requirements:No special requirements.
Program Release Status: New Release
Program Install Support: Install and Uninstall