title: RNAMethPre: A Web Server for the Prediction and Query of mRNA m6A Sites.
abstract: 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.
authors.affiliation: MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.
authors.forename: Shunian
authors.initials: S
authors.lastname: Xiang
authors.affiliation: MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.|Department of Statistics, University of California, Berkeley, California, 94720, United States of America.
authors.forename: Ke
authors.initials: K
authors.lastname: Liu
authors.affiliation: MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.
authors.forename: Zhangming
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Beijing, 518055, P. R. China.
authors.forename: Yaou
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.
authors.forename: Zhirong
authors.initials: Z
authors.lastname: Sun
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000235:genetics / Q000378:metabolism; D000818:Animals; D030541:Databases, Genetic; D006801:Humans; D051379:Mice; D012323:RNA Processing, Post-Transcriptional / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000502:physiology*
chemical_list: D012333:RNA, Messenger; C010223:N-methyladenosine; D000241:Adenosine