M6APred-EL: A Sequence-Based Predictor for Identifying N6-methyladenosine Sites Using Ensemble Learning

N6-methyladenosine (m(6)A) modification is the most abundant RNA methylation modification and involves various biological processes, such as RNA splicing and degradation. Recent studies have demonstrated the feasibility of identifying m(6)A peaks using high-throughput sequencing techniques. However, such techniques cannot accurately identify specific methylated sites, which is important for a better understanding of m(6)A functions. In this study, we develop a novel machine learning-based predictor called M6APred-EL for the identification of m(6)A sites. To predict m(6)A sites accurately within genomic sequences, we trained an ensemble of three support vector machine classifiers that explore the position-specific information and physical chemical information from position-specific k-mer nucleotide propensity, physical-chemical properties, and ring-function-hydrogen-chemical properties. We examined and compared the performance of our predictor with other state-of-the-art methods of benchmarking datasets. Comparative results showed that the proposed M6APred-EL performed more accurately for m(6)A site identification. Moreover, a user-friendly web server that implements the proposed M6APred-EL is well established and is currently available at http://server.malab.cn/M6APred-EL/. It is expected to be a practical and effective tool for the investigation of m(6)A functional mechanisms.