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###### MD Parameter based Tm Predictor

It is a melting temperature predicter for DNA sequences based on a simple phenomenological model of DNA denaturation. It takes into account the stacking and hydrogen bonding interaction (as DNA strength parameter), length of the sequence, the salt concentration (taken as [Na+]) and nucleotide strand concentration (taken in g/ml) to predict the melting temperature.

 Read the DNA sequence from one end to the other & add up the DNA strength parameter (Given in table 1). ↓ Calculate the strength parameter per base (E) as: E = DNA strength parameter ⁄ Length of sequence ↓ Substitute the value of E, the length of sequence (which is 70 basepair in this case), the Na+ ion concentration and the nucleotide strand concentration in the given equation.Tm (°C) = {(-8.69 × E) + [ 6.07 × ln(Len) ] + [4.97 × ln(Conc)] + [1.11 × ln(DNA)]} - 233.45 This gives the melting temperature for a 70 bp window. ↓ The above procedure is repeated for the complete sequence with a step-size of one bp. Figure:Flow chart to calculate the melting temperature

Table 1.Energy Parameters for dinucleotides derived from molecular dynamics simulations(kcal/mol).

 Dinucleotide Hydrogen Bond Stacking Energy Strength Parameter AA -6.92 -26.92 -33.84 AC -9.64 -27.89 -37.51 AG -8.78 -26.91 -35.69 AT -7.05 -27.33 -34.38 CA -9.34 -27.23 -36.57 CC -44.84 -26.33 -38.17 CG -11.37 -27.83 -39.20 CT -8.78 -26.91 -35.69 GA -10.12 -26.98 -37.10 GC -12.03 -28.27 -40.30 GG -11.84 -26.33 -38.17 GT -9.64 -27.87 -37.51 TA -7.16 -27.15 -34.31 TC -10.12 26.98 -37.10 TG -9.34 -27.23 -36.57 TT -6.92 -26.92 -33.84