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Open Access Software

MELTING, a flexible platform to predict the melting temperatures of nucleic acids

Marine Dumousseau, Nicolas Rodriguez, Nick Juty and Nicolas Le Novère*

Author Affiliations

EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB10 1SD, UK

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BMC Bioinformatics 2012, 13:101  doi:10.1186/1471-2105-13-101

Published: 16 May 2012

Additional files

Additional file 1:

MELTING 5 thermodynamic formulae and parameters. This additional file lists all the patterns which can be managed by MELTING 5 and the references of each matching thermodynamic formulae and parameters. MELTING 5 cannot currently compute terminal mismatches, all mismatches must be internal. You can refer to the documentation in the MELTING 5 package or at the following page (http://www.ebi.ac.uk/compneur-srv/melting/melting5-doc/melting.html webcite) to have more information about the MELTING 5 implementation of the thermodynamic formulae.

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Additional file 2:

Ion corrections. This additional file lists all the ion corrections which can be applied by MELTING 5 and MELTING 4.3 as well as the references of each matching ion correction. You can refer to the documentation in the MELTING 5 package or at the following page (http://www.ebi.ac.uk/compneur-srv/melting/melting5-doc/melting.html webcite) to have more information about the MELTING 5 implementation of the ion corrections.

Format: XLS Size: 12KB Download file

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Additional file 3:

Figure S1. MELTING results for RNA sequences. The various predictions were computed for 16 different not self-complementary RNA sequences from Xia et al. [[39]]. The sodium concentration was 1 M and the oligomer concentration 0.0002 M. The thermodynamic parameters with which the melting temperature was computed were Freier et al. [[40]] (fre86) and Xia et al. [[39]] (xia98).

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Additional file 4:

Figure S2. MELTING results for DNA/RNA duplexes. The various predictions were computed for 29 different DNA/RNA duplexes from Sugimoto et al. [[41]]. The sodium concentration was 1 M and the oligomer concentration 0.0001 M. The thermodynamic parameters with which the melting temperature was computed were Sugimoto et al. [[41]] (sug95).

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Additional file 5:

Figure S3. MELTING results for RNA self complementary sequences. The various predictions were computed for 36 different RNA self complementary sequences from Xia et al. (1998) [[39]]. The sodium concentration was 1 M and the oligomer concentrations 0.0001 M. The thermodynamic parameters with which the melting temperature was computed were Freier et al. [[40]] (fre86) and Xia et al. [[39]] (xia98).

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Additional file 6:

Features comparison of MELTING with similar softwares. This additional file lists the software structure information, the supported hybridization and parameters, the ion and denaturing corrections, the approximative formulae and the supported duplex patterns of MELTING and other similar softwares.

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