RNAMethPre: A Web Server for the Prediction and Query of mRNA m6A Sites

N6-Methyladenosine (m6A) is the most common mRNA modification; it occurs in a wide range of taxon and is associated with many key biological processes. High-throughput experiments have identified m6A-peaks and sites across the transcriptome, but studies of m6A sites at the transcriptome-wide scale are limited to a few species and tissue types. Therefore, the computational prediction of mRNA m6A sites has become an important strategy. In this study, we integrated multiple features of mRNA (flanking sequences, local secondary structure information, and relative position information) and trained a SVM classifier to predict m6A sites in mammalian mRNA sequences. Our method achieves ideal performance in both cross-validation tests and rigorous independent dataset tests. The server also provides a comprehensive database of predicted transcriptome-wide m6A sites and curated m6A-seq peaks from the literature for both human and mouse, and these can be queried and visualized in a genome browser. The RNAMethPre web server provides a user-friendly tool for the prediction and query of mRNA m6A sites, which is freely accessible for public use at http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html.N6-甲基腺嘌呤（N6-Methyladenosine，m6A）是目前最常见的信使RNA（messenger RNA，mRNA）修饰形式，广泛分布于各类生物类群，并与诸多关键生物学过程密切相关。高通量实验已在全转录组范围内鉴定出m6A修饰峰与修饰位点，但全转录组规模的m6A位点研究仅局限于少数物种与组织类型。因此，mRNA m6A位点的计算预测已成为重要的研究策略。本研究整合了mRNA的多项特征：侧翼序列、局部二级结构信息以及相对位置信息，并训练了支持向量机（Support Vector Machine，SVM）分类器，以预测哺乳动物mRNA序列中的m6A位点。本方法在交叉验证测试与严格的独立数据集测试中均取得了理想的预测性能。该服务器还搭建了一个综合数据库，涵盖人类与小鼠的全转录组预测m6A位点，以及经文献整理的m6A测序（m6A-seq）峰数据，用户可通过基因组浏览器对这些数据进行查询与可视化。RNAMethPre网页服务器为mRNA m6A位点的预测与查询提供了便捷易用的工具，公众可通过http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html免费访问使用。