Primer design program for visualising and calculating secondary structure stability
The program utilizes Thermodynamic data, specified by SantaLucia et al (1998) to calculate melting Temperature and Secondary Structure stabilities. For specific description and complete algorithm please refer to the source code and study paper. In the process of creating this program, the study has look at many different primer design programs available online such as Primer3, Biophp, Oligo Analyzer (IDTDNA), OligoCalculator(Sigma Aldrich) and many others. While all of the more popular ones uses nearest neighbour (NN) model, not all of them agree on the same formula, parameters, or even salt correction factors, which can have great difference in the final results. This problem is eventually further exarcebated when these programs are not open-sourced, or even worse, difficult to understand. Ultimately, while this program has attempted to find the best possible algorithm, it by no means should be seen as better or worse than other programs. In fact it is best to use this program in conjunction with other available and up to date programs to get the most informative decision.
Le Hai, LSHTM 2018-2019, Michael Miles group