Predicting Polymerase Chain Reaction Success: Integrating the K-Word Order Model, Physicochemical Properties Modeling...

Polymerase Chain Reaction (PCR) has been a pivotal scientific technique since the twentieth century, and it is widely applied across various domains. Despite its ubiquity, challenges persist in efficiently amplifying specific DNA templates.

While PCR experimental procedures have garnered significant attention, the analysis of the DNA template, which is the experiment's focal point, has been notably overlooked. This study addresses the uncertainty surrounding the amplification of DNA fragments using conventional Taq DNA polymerase-based PCR protocols. The imperative need to characterize DNA templates and devise a reliable method for predicting PCR success is underscored.

In this study, we formulate a 72-dimensional feature vector representing a DNA template through the utilization of k-word order and modeling of physicochemical properties of double bases. Subsequently, a Support Vector Machine (SVM) model is employed to assess PCR results.

A jackknife cross-validation test is used to evaluate the anticipated success rates, resulting in an overall accuracy of 95.77%. Sensitivity, specificity, and Matthew's Correlation Coefficient (MCC) stand at 95.75%, 95.79%, and 0.915, respectively.