iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple genomes

Summary 5hmC, 6mA and 4mC are three common DNA modifications and involve in various of biological processes. Accurate genome-wide identification of these sites is invaluable for better understanding their biological functions. Due to the labor-intensive and expensive nature of experimental methods, it is urgent to develop computational methods for the genome-wide detection of these sites. Keeping this in mind, the current study was devoted to construct a computational method to identify 5hmC, 6mA and 4mC. We initially used K-tuple nucleotide component, nucleotide chemical property and nucleotide frequency, and mono-nucleotide binary encoding scheme to formulate samples. Subsequently, random forest was utilized to identify 5hmC, 6mA and 4mC sites. Cross-validated results showed that the proposed method could produce the excellent generalization ability in the identification of the three modification sites. Based on the proposed model, a web-server called iDNA-MS was established and is freely accessible at http://lin-group.cn/server/iDNA-MS.