title: Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions.
abstract: 2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation.
authors.affiliation: Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China. Electronic address: chenweiimu@gmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: School of Public Health, North China University of Science and Technology, Tangshan 063000, China.
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.affiliation: Department of Pathophysiology, Sichuan Medical University, Luzhou 646000, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Tang
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: hlin@uestc.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D019295:Computational Biology; D003562:Cytidine / Q000031:analogs & derivatives / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D008745:Methylation; D008780:Methyltransferases / Q000235:genetics; D051379:Mice; D009711:Nucleotides / Q000235:genetics*; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D060388:Support Vector Machine
chemical_list: D009711:Nucleotides; C052203:2'-O-methylcytidine; D003562:Cytidine; D008780:Methyltransferases
keywords: 2′-O-methylationation; Nucleotide chemical property; Nucleotide composition; Support vector machine