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MeltSim: The DNA Melting Simulator
Since 1980

Overview: The DNA Melting Algorithm

MeltSim is a statistical-mechanical program for calculating melting (denaturation) curves (derivative profiles) and maps of DNA, from genes to genomes. The model is the one-dimensional Ising lattice to which loop entropy has been appended [1][2][3]. The original algorithm is that of Poland & Scheraga [4] and Poland [5], with the Fixman & Friere approximation of the loop entropy by a sum of exponentials [6]. Parameters in Poland's original algorithm were evaluated by Blake & Delcourt [7][8] and provide near-quantitative agreement between observed and calculated Tm, amplitudes, breadths, and areas of transitions obtained under equilibrium conditions.


The seminal publication:

Blake, R.D., Bizzaro, J.W., Blake, J.D., Day, G.R., Delcourt, S.G., Knowles, J., Marx, K.A. and SantaLucia, J., Jr. 1999. Statistical Mechanical Simulation of Polymeric DNA Melting with MELTSIM. Bioinformatics 15(5):370-375. |Abstract| |Full Free Text| |PubMed ID: 10366657|

Publications based on (or research that made use of) MeltSim (or related work by R.D. Blake):

Rasmussen, J.P., Saint, C.P. and Monis, P.T. 2007. Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes. BMC Bioinformatics 8:107. |Abstract| |Full Free Text| |PubMed ID: 17391531|

Tostesen, E., Jerstad, G.I. and Hovig, E. 2005. analysis of partly melted DNA conformations using stitch profiles. Nucleic Acids Res 33:W573-6. |Abstract| |Full Free Text| |PubMed ID: 15980539|

Tostesen, E. 2005. Partly melted DNA conformations obtained with a probability peak finding method. Phys Rev E 71:061922. |Abstract| |Full Free Text| |PubMed ID: 16089780|

Long, D.D., Grosse, I. and Marx, K.A. 2004. Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophys Chem 110(1-2):25-38. |Abstract| |PubMed ID: 15223141|

Metzler, R. and Ambjornsson, T. 2004. Dynamic approach to DNA breathing. Biophys Chem. |Full Free Text|

Garel, T. and Orland, H. 2003. On the role of mismatches in DNA denaturation. arXiv:cond-mat/0304080. |Abstract| |Full Free Text|

Blossey, R. and Carlon, E. 2003. Reparametrizing the loop entropy weights: Effect on DNA melting curves. Phys Rev E 68:061911. |Abstract| |Full Free Text| |PubMed ID: 14754238|

Marx, K.A., Bizzaro, J.W., Blake, R.D., Hsien Tsai, M. and Feng Tao, L. 2000. Experimental DNA Melting Behavior of the Three Major Schistosoma Species. Mol Biochem Parasitol 107(2):303-307. |PubMed ID: 10779607|

Marx, K.A., Assil, I.Q., Bizzaro, J.W. and Blake, R.D. 1998. Comparison of Experimental to MELTSIM Calculated DNA Melting of the (A+T) Rich Dictyostelium discoideum Genome: Denaturation Maps Distinguish Exons From Introns. J Biomol Struct Dyn 16(2):329-339. |PubMed ID: 9833671|

Blake, R.D. and Delcourt, S.G. 1998. Thermal stability of DNA. Nucleic Acids Research 26(14):3323-3332. |Abstract| |Full Free Text| |PubMed ID: 9649614|

Bizzaro, J.W., Marx, K.A. and Blake, R.D. 1997. Comparison of Experimental with Theoretical Melting of the Yeast Genome and Individual Yeast Chromosome Denaturation Mapping Using the Program MELTSIM. Materials Research Society Symposium Proceedings 489:73-77.

Marx, K.A., Bizzaro, J.W., Assil, I.Q. and Blake, R.D. 1996. Comparison of Experimental and Theoretical Melting Behavior of DNA. Materials Research Society Symposium Proceedings 463:147-152.

If you have any other publications based on MeltSim, please email us.


Mailing List

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See Also

Dan is an open-source module for EMBOSS, which calculates Tm and %GC for sequences within a moving window. A web interface is available at the link given.

MELTING is an open-source command-line program, which calculates Tm for short (< 60 bp) sequences. A web interface is available at the link given.

POLAND is a Web tool that calculates the thermal denaturation profile of double-stranded RNA, DNA or RNA/DNA-hybrids based on sequence input and parameter settings.

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  1. Ising, E. 1925. Physik 31:253.
  2. Hill, T.L. 1956. In Statistical Mechanics. McGraw-Hill, New York. (book out of print)
  3. Wartell, R.M. & Benight, A.S. 1985. Physics Rep 126:67-107.
  4. Poland, D. & Scheraga, H.A. 1970. In Theory of Helix-Coil Transitions in Biopolymers. Academic Press, New York. (book out of print)
  5. Poland, D. 1974. Biopolymers 13:1859-1871.
  6. Fixman, M. & Friere, J. 1977. Biopolymers 16:2693-2704.
  7. Delcourt, S.G. & Blake, R.D. 1991. Stacking Energies in DNA. J Biol Chem 266(23):15160-15169.
  8. Blake, R.D. & Delcourt, S.G. 1998. Thermal stability of DNA. Nucleic Acids Research 26(14):3323-3332.