m6AmPred: Identifying RNA N6, 2′-O-dimethyladenosine (m6Am) sites based on sequence-derived information

N6,2'-O-dimethyladenosine (m(6)A(m)) is a reversible modification widely occurred on varied RNA molecules. The biological function of m(6)A(m) is yet to be known though recent studies have revealed its influences in cellular mRNA fate. Precise identification of m(6)A(m) sites on RNA is vital for the understanding of its biological functions. We present here m6AmPred, the first web server for in silico identification of m(6)A(m) sites from the primary sequences of RNA. Built upon the eXtreme Gradient Boosting with Dart algorithm (XgbDart) and EIIP-PseEIIP encoding scheme, m6AmPred achieved promising prediction performance with the AUCs greater than 0.954 when tested by 10-fold cross-validation and independent testing datasets. To critically test and validate the performance of m6AmPred, the experimentally verified m(6)A(m) sites from two data sources were cross-validated. The m6AmPred web server is freely accessible at: https://www.xjtlu.edu.cn/biologicalsciences/m6am, and it should make a useful tool for the researchers who are interested in N6,2'-O-dimethyladenosine RNA modification.

Automated summary

N6,2'-O-dimethyladenosine (m(6)A(m)) is a reversible modification found on various RNA molecules, and its biological function is still unknown. In order to identify m(6)A(m) sites on RNA and aid researchers in understanding its biological functions, m6AmPred, the first web server for in silico prediction of m(6)A(m) sites from RNA sequences, has been developed using the eXtreme Gradient Boosting with Dart algorithm (XgbDart) and EIIP-PseEIIP encoding scheme.