title: iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition.
abstract: Occurring at adenine (A) with the consensus motif GAC, N(6)-methyladenosine (m(6)A) is one of the most abundant modifications in RNA, which plays very important roles in many biological processes. The nonuniform distribution of m(6)A sites across the genome implies that, for better understanding the regulatory mechanism of m(6)A, it is indispensable to characterize its sites in a genome-wide scope. Although a series of experimental technologies have been developed in this regard, they are both time-consuming and expensive. With the avalanche of RNA sequences generated in the postgenomic age, it is highly desired to develop computational methods to timely identify their m(6)A sites. In view of this, a predictor called "iRNA-Methyl" is proposed by formulating RNA sequences with the "pseudo dinucleotide composition" into which three RNA physiochemical properties were incorporated. Rigorous cross-validation tests have indicated that iRNA-Methyl holds very high potential to become a useful tool for genome analysis. For the convenience of most experimental scientists, a web-server for iRNA-Methyl has been established at http://lin.uestc.edu.cn/server/iRNA-Methyl by which users can easily get their desired results without needing to go through the mathematical details.
authors: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063009, China; Gordon Life Science Institute, Belmont, MA 02478, USA. Electronic address: chenweiimu@gmail.com.
authors: Wei
authors: W
authors: Chen
authors: School of Public Health, North China University of Science and Technology, Tangshan 063000, China.
authors: Pengmian
authors: P
authors: Feng
authors: School of Public Health, North China University of Science and Technology, Tangshan 063000, China.
authors: Hui
authors: H
authors: Ding
authors: Gordon Life Science Institute, Belmont, MA 02478, USA; 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: Hao
authors: H
authors: Lin
authors: Gordon Life Science Institute, Belmont, MA 02478, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: kcchou@gordonlifescience.org.
authors: Kuo-Chen
authors: KC
authors: Chou
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000032:analysis / Q000378:metabolism; D000465:Algorithms; D001665:Binding Sites; D019277:Entropy; D057890:Epigenomics / Q000379:methods; D016680:Genome, Bacterial; D020407:Internet; D000069550:Machine Learning; D008745:Methylation; D008780:Methyltransferases / Q000378:metabolism*; D008958:Models, Molecular; D059372:Nucleotide Motifs; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; C010223:N-methyladenosine; D008780:Methyltransferases; C022556:mRNA (2'-O-methyladenosine-N6-)-methyltransferase; D000241:Adenosine
keywords: Flexible scaled window; Global sequence pattern; Pseudo dinucleotide composition: PseKNC; RNA methylation