Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability


DNA melting bubbles are the idea of the many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Though prediction of duplex stability with the closest neighbor (NN) technique is abundant faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we tend to thought of that PBD predicted TIDD is inherently connected to the intrinsic duplex stabilities of destabilization regions. We tend to show by regression modeling that NN duplex stabilities can be used to predict TIDD nearly as accurately as is predicted with PBD. Predicted TIDD is after all ascribed to non-linear transformation of NN duplex stabilities in destabilization regions plus effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models gift an accessible tool for researchers. TIDD can be predicted on our webserver at

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