* [[http://www.bioinformatics.org/ftp/pub/meltsim/meltsim-1.99.0.tar.gz | Download MeltSim 1.99.0 for the command-line]] (1998 parameters)

->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. |[[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1851973&rendertype=abstract | Abstract]]%newwin%| |[[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17391531 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17391531 | PubMed ID: 17391531]]%newwin%|

If you have any other publications based on MeltSim, please [[http://www.bioinformatics.org/lists/meltsim | email us]].

* [[ftp://ftp.bioinformatics.org/pub/meltsim/meltsim-1.99.0.tar.gz | MeltSim 1.99.0 for the command-line]] (1998 parameters)

* [[MeltSimWin | MeltSim 1.0-beta for Windows]] (1995 parameters)

[[http://www.biophys.uni-duesseldorf.de/local/POLAND/poland.html | 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.

Direct questions or comments to [[http://www.bioinformatics.org/lists/meltsim | the mailing list]].

->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. |[[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1851973&rendertype=abstract | Abstract]]%newwin%| |[[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17391531 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17391531 | PubMed ID: 17391531]]%newwin%|

->Metzler, R. and Ambjornsson, T. 2004. Dynamic approach to DNA breathing. ''Biophys Chem''. |[[http://www.nordita.dk/preprints/2004/200495.pdf | Full Free Text]]%newwin%|

''Since 1980''

->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. |[[http://bioinformatics.oupjournals.org/cgi/content/abstract/15/5/370 | Abstract]]%newwin%| |[[http://bioinformatics.oupjournals.org/cgi/reprint/15/5/370 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=10366657&dopt=Abstract | PubMed ID: 10366657]]%newwin%|

->Tostesen, E., Jerstad, G.I. and Hovig, E. 2005. Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles. ''Nucleic Acids Res'' '''33''':W573-6. |[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1160185&rendertype=abstract | Abstract]]%newwin%| |[[http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15980539 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15980539 | PubMed ID: 15980539]]%newwin%|

->Tostesen, E. 2005. Partly melted DNA conformations obtained with a probability peak finding method. ''Phys Rev E'' '''71''':061922. |[[http://arxiv.org/abs/q-bio.BM/0404019 | Abstract]]%newwin%| |[[http://arxiv.org/pdf/q-bio.BM/0404019 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16089780 | PubMed ID: 16089780]]%newwin%|

->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. |[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFB-4C8NRFM-2&_user=10&_handle=V-WA-A-W-AD-MsSAYVA-UUA-U-AAWVYEYCED-AAWWVDEBED-WVCYWEAEC-AD-U&_fmt=summary&_coverDate=07%2F01%2F2004&_rdoc=3&_orig=browse&_srch=%23toc%235222%232004%23998899998%23507237!&_cdi=5222&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=83bb00d6c4c65a3a523066b929d54628 | Abstract]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15223141&query_hl=4 | PubMed ID: 15223141]]%newwin%|

->Metzler, R. and Ambjornsson, T. 2004. Dynamic approach to DNA breathing. ''Biophys Chem'' (in press). |[[http://www.nordita.dk/preprints/2004/200495.pdf | Full Free Text]]%newwin%|

->Garel, T. and Orland, H. 2003. On the role of mismatches in DNA denaturation. arXiv:cond-mat/0304080. |[[http://arxiv.org/abs/cond-mat/0304080 | Abstract]]%newwin%| |[[http://arxiv.org/pdf/cond-mat/0304080 | Full Free Text]]%newwin%|

->Blossey, R. and Carlon, E. 2003. Reparametrizing the loop entropy weights: Effect on DNA melting curves. ''Phys Rev E'' '''68''':061911. |[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000068000006061911000001&idtype=cvips&gifs=yes | Abstract]]%newwin%| |[[http://arxiv.org/pdf/cond-mat/0212457 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14754238 | PubMed ID: 14754238]]%newwin%|

->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. |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10779607 | PubMed ID: 10779607]]%newwin%|

->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. |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9833671&query_hl=5 | PubMed ID: 9833671]]%newwin%|

->Blake, R.D. and Delcourt, S.G. 1998. Thermal stability of DNA. ''Nucleic Acids Research'' '''26'''(14):3323-3332. |[[http://nar.oxfordjournals.org/cgi/content/abstract/26/14/3323 | Abstract]]%newwin%| |[[http://nar.oxfordjournals.org/cgi/content/full/26/14/3323 | Full Free Text]]%newwin%| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9649614 | PubMed ID: 9649614]]%newwin%|

Direct questions or comments to: [[mailto:meltsim@bioinformatics.org | meltsim@bioinformatics.org]].

! 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 [[#ising|#]][[#hill|#]][[#wartel|#]]. The original algorithm is that of Poland & Scheraga [[#poland_book|#]] and Poland [[#poland_article|#]], with the Fixman & Friere approximation of the loop entropy by a sum of exponentials [[#fixman|#]]. Parameters in Poland's original algorithm were evaluated by Blake & Delcourt [[#delcourt|#]][[#blake|#]] and provide near-quantitative agreement between observed and calculated T'_m_', amplitudes, breadths, and areas of transitions obtained under equilibrium conditions.


!! Publications

'''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. |[[http://bioinformatics.oupjournals.org/cgi/content/abstract/15/5/370 | Abstract]]| |[[http://bioinformatics.oupjournals.org/cgi/reprint/15/5/370 | Full Free Text]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=10366657&dopt=Abstract | PubMed ID: 10366657]]|

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

->Tostesen, E., Jerstad, G.I. and Hovig, E. 2005. Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles. ''Nucleic Acids Res'' '''33''':W573-6. |[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1160185&rendertype=abstract | Abstract]]| |[[http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15980539 | Full Free Text]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15980539 | PubMed ID: 15980539]]|

->Tostesen, E. 2005. Partly melted DNA conformations obtained with a probability peak finding method. ''Phys Rev E'' '''71''':061922. |[[http://arxiv.org/abs/q-bio.BM/0404019 | Abstract]]| |[[http://arxiv.org/pdf/q-bio.BM/0404019 | Full Free Text]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16089780 | 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. |[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFB-4C8NRFM-2&_user=10&_handle=V-WA-A-W-AD-MsSAYVA-UUA-U-AAWVYEYCED-AAWWVDEBED-WVCYWEAEC-AD-U&_fmt=summary&_coverDate=07%2F01%2F2004&_rdoc=3&_orig=browse&_srch=%23toc%235222%232004%23998899998%23507237!&_cdi=5222&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=83bb00d6c4c65a3a523066b929d54628 | Abstract]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15223141&query_hl=4 | PubMed ID: 15223141]]|

->Metzler, R. and Ambjornsson, T. 2004. Dynamic approach to DNA breathing. ''Biophys Chem'' (in press). |[[http://www.nordita.dk/preprints/2004/200495.pdf | Full Free Text]]|

->Garel, T. and Orland, H. 2003. On the role of mismatches in DNA denaturation. arXiv:cond-mat/0304080. |[[http://arxiv.org/abs/cond-mat/0304080 | Abstract]]| |[[http://arxiv.org/pdf/cond-mat/0304080 | Full Free Text]]|

->Blossey, R. and Carlon, E. 2003. Reparametrizing the loop entropy weights: Effect on DNA melting curves. ''Phys Rev E'' '''68''':061911. |[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000068000006061911000001&idtype=cvips&gifs=yes | Abstract]]| |[[http://arxiv.org/pdf/cond-mat/0212457 | Full Free Text]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14754238 | 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. |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10779607 | 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. |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9833671&query_hl=5 | PubMed ID: 9833671]]|

->Blake, R.D. and Delcourt, S.G. 1998. Thermal stability of DNA. ''Nucleic Acids Research'' '''26'''(14):3323-3332. |[[http://nar.oxfordjournals.org/cgi/content/abstract/26/14/3323 | Abstract]]| |[[http://nar.oxfordjournals.org/cgi/content/full/26/14/3323 | Full Free Text]]| |[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9649614 | 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 [[mailto:meltsim@bioinformatics.org | email us]].

!! Versions

* [[MeltSimWin | MeltSim 1.0-beta for Windows]] \\
(Now licensed under the GNU GPL.)

!! Mailing List

If you would like to subscribe to the mailing list for general discussions about MeltSim, [[http://bioinformatics.org/mailman/listinfo/meltsim/ | click here]].

!! See Also

[[http://bioweb.pasteur.fr/seqanal/interfaces/dan.html | Dan]] is an open-source module for EMBOSS, which calculates T'_m_' and %GC for sequences within a moving window. A web interface is available at the link given.

[[http://www.ebi.ac.uk/~lenov/meltinghome.html | MELTING]] is an open-source command-line program, which calculates T'_m_' for short (< 60 bp) sequences. A web interface is available at the link given.

Direct questions or comments to: [[mailto:jeff@bioinformatics.org | jeff@bioinformatics.org]].

!! References

# [[#ising]]%newwin% Ising, E. 1925. ''Physik'' '''31''':253.
# [[#hill]]%newwin% Hill, T.L. 1956. In ''Statistical Mechanics''. McGraw-Hill, New York. (book out of print)
# [[#wartel]]%newwin% Wartell, R.M. & Benight, A.S. 1985. ''Physics Rep'' '''126''':67-107.
# [[#poland_book]]%newwin% Poland, D. & Scheraga, H.A. 1970. In ''Theory of Helix-Coil Transitions in Biopolymers''. Academic Press, New York. (book out of print)
# [[#poland_article]]%newwin% Poland, D. 1974. ''Biopolymers'' '''13''':1859-1871.
# [[#fixman]]%newwin% Fixman, M. & Friere, J. 1977. ''Biopolymers'' '''16''':2693-2704.
# [[#delcourt]]%newwin% Delcourt, S.G. & Blake, R.D. 1991. Stacking Energies in DNA. ''J Biol Chem'' '''266'''(23):15160-15169.
# [[#blake]]%newwin% Blake, R.D. & Delcourt, S.G. 1998. Thermal stability of DNA. ''Nucleic Acids Research'' '''26'''(14):3323-3332.