AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana. Issue 11 (23rd August 2016)

• Record Type: Journal Article
• Authors: Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong
• Is Part Of: Molecular bioSystems. Volume 12:Issue 11(2016:Nov.)
• Page Start: 3333
• Page End: 3337
• Publication Date: 2016-08-23
• Subjects: Molecular biology -- Periodicals; Biochemistry -- Periodicals; 571.7405
• DOI: 10.1039/c6mb00536e
• Languages: English
• ISSNs: 1742-206X

Abstract

Abstract : The first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites. Abstract : N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k -mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. 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 query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at ; Web:http://bioinfo.tsinghua.edu.cn/AthMethPre/index.html .