Distance-based Support Vector Machine to Predict DNA N6-methyladenine Modification

DNA N6-methyladenine plays an important role in the restriction-modification system to isolate invasion from adventive DNA. The shortcomings of the high time consumption and high costs of experimental methods have been exposed, and some computational methods have emerged. The support vector machine theory has received extensive attention in the bioinformatics field due to its solid theoretical foundation and many good characteristics.

General machine learning methods include an important step of extracting features. The research has omitted this step and replaced with easy-to-obtain sequence distances matrix to obtain better results. Method: First sequence alignment technology was used to achieve the similarity matrix. Then, a novel transformation turned the similarity matrix into a distance matrix. Next, the similarity-distance matrix was made positive semi-definite so that it can be used in the kernel matrix. Finally, the LIBSVM software was applied to solve the support vector machine.