Table 5.

Model training

Require: A thermodynamic model T, an input set S with perfect match DNA duplexes.

Ensure: An optimal set of thermodynamic DNA parameters X for the input model

1: Initialize counts matrix F with zeros for all unique doublets/triplets

2: Initialize results matrix R with experimentally approximated free energies for each duplex

3: for i = 0 to ||S|| do

4:    Count unique doublets/triplets in duplex S[i] and update F

5: end for

6: Solve the equation X = arg minX (F × X - R)2

7: return X