title: MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
abstract: BACKGROUND
  Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and the optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, and microarrays. MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids. MELTING 4.2 was able to handle several types of hybridization such as DNA/DNA, RNA/RNA, DNA/RNA and provided corrections to melting temperatures due to the presence of sodium. The program can use either an approximative approach or a more accurate Nearest-Neighbor approach.
  
  
  RESULTS
  Two new versions of the MELTING software have been released. MELTING 4.3 is a direct update of version 4.2, integrating newly available thermodynamic parameters for inosine, a modified adenine base with an universal base capacity, and incorporates a correction for magnesium. MELTING 5 is a complete reimplementation which allows much greater flexibility and extensibility. It incorporates all the thermodynamic parameters and corrections provided in MELTING 4.x and introduces a large set of thermodynamic formulae and parameters, to facilitate the calculation of melting temperatures for perfectly matching sequences, mismatches, bulge loops, CNG repeats, dangling ends, inosines, locked nucleic acids, 2-hydroxyadenines and azobenzenes. It also includes temperature corrections for monovalent ions (sodium, potassium, Tris), magnesium ions and commonly used denaturing agents such as formamide and DMSO.
  
  
  CONCLUSIONS
  MELTING is a useful and very flexible tool for predicting melting temperatures using approximative formulae or Nearest-Neighbor approaches, where one can select different sets of Nearest-Neighbor parameters, corrections and formulae. Both versions are freely available at http://sourceforge.net/projects/melting/and at http://www.ebi.ac.uk/compneur-srv/melting/under the terms of the GPL license.
authors.affiliation: EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, UK.
authors.forename: Marine
authors.initials: M
authors.lastname: Dumousseau
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rodriguez
authors.forename: Nick
authors.initials: N
authors.lastname: Juty
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
mesh_terms: D004247:DNA / Q000737:chemistry; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization / Q000379:methods; D009696:Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012984:Software; D013696:Temperature; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D009696:Nucleic Acids; D012313:RNA; D004247:DNA