RNAMethPre: A web server for the prediction and query of mRNAm6A sites

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© 2016 Xiang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. N 6 -Methyladenosine (m 6 A) 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 m 6 A-peaks and sites across the transcriptome, but studies of m 6 A sites at the transcriptome-wide scale are limited to a few species and tissue types. Therefore, the computational prediction of mRNA m 6 A 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 m 6 A 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 m 6 A sites and curated m 6 A-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 m 6 A sites, which is freely accessible for public use at http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html.




Xiang, S., Liu, K., Yan, Z., Zhang, Y., & Sun, Z. (2016). RNAMethPre: A web server for the prediction and query of mRNAm6A sites. PLoS ONE, 11(10). https://doi.org/10.1371/journal.pone.0162707

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