摘要：Summary5hmC, 6mA, and 4mC are three common DNA modifications and are involved in various of biological processes. Accurate genome-wide identification of these sites is invaluable for better understanding their biological functions. Owing 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 usedK-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 athttp://lin-group.cn/server/iDNA-MS.Graphical AbstractDisplay OmittedHighlights•A computational tool was developed for identification of 5hmC, 6mA, and 4mC•6mA and 4mC mark similar regions in theC. equisetifoliaandF. vescagenomes•5hmC enriches in the initial and middle of the DNA loops•A user-friendly webserver was available athttp://lin-group.cn/server/iDNA-MSGenetics; Quantitative Genetics; Bioinformatics
