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Table 5 Model training

From: Free energy estimation of short DNA duplex hybridizations

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 min X (F × X - R)2
7: return X