iDHS-DSAMS: Identifying DNase I hypersensitive sites based on the dinucleotide property matrix and ensemble bagged tree.

DNase I hypersensitive site (DHS) is related to DNA regulatory elements, so the understanding of DHS sites is of great significance for biomedical research. However, traditional experiments are not very good at identifying recombinant sites of a large number of emerging DNA sequences by sequencing. Some machine learning methods have been proposed to identify DHS, but most methods ignore spatial autocorrelation of the DNA sequence. In this paper, we proposed a predictor called iDHS-DSAMS to identify DHS based on the benchmark datasets. We develop a feature extraction method called dinucleotide-based spatial autocorrelation (DSA). Then we use Min-Redundancy-Max-Relevance (mRMR) to remove irrelevant and redundant features and a 100-dimensional feature vector is selected. Finally, we utilize ensemble bagged tree as classifier, which is based on the oversampled datasets using SMOTE. Five-fold cross validation tests on two benchmark datasets indicate that the proposed method outperforms its existing counterparts on the individual accuracy (Acc), Matthews correlation coefficient (MCC), sensitivity (Sn) and specificity (Sp).