title: iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences.
abstract: Catalyzed by adenosine deaminase (ADAR), the adenosine to inosine (A-to-I) editing in RNA is not only involved in various important biological processes, but also closely associated with a series of major diseases. Therefore, knowledge about the A-to-I editing sites in RNA is crucially important for both basic research and drug development. Given an uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which one of them can be of A-to-I editing, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such an important problem based on the RNA sequence information alone. To fill this empty area, we have proposed a predictor called iRNA-AI by incorporating the chemical properties of nucleotides and their sliding occurrence density distribution along a RNA sequence into the general form of pseudo nucleotide composition (PseKNC). It has been shown by the rigorous jackknife test and independent dataset test that the performance of the proposed predictor is quite promising. For the convenience of most experimental scientists, a user-friendly web-server for iRNA-AI has been established at http://lin.uestc.edu.cn/server/iRNA-AI/, by which users can easily get their desired results without the need to go through the mathematical details.
authors.affiliation: Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Tangshan, China.|Gordon Life Science Institute, Belmont, Massachusetts, United States of America.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, China.
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Yang
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.|Gordon Life Science Institute, Belmont, Massachusetts, United States of America.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.|Gordon Life Science Institute, Belmont, Massachusetts, United States of America.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000241:Adenosine / Q000737:chemistry* / Q000235:genetics; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D007288:Inosine / Q000737:chemistry* / Q000235:genetics; D017393:RNA Editing; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D060388:Support Vector Machine
chemical_list: D012333:RNA, Messenger; D007288:Inosine; D000241:Adenosine
keywords: A-to-I editing; PseKNC; nucleotide chemical properties; nucleotide density distribution; web-server