iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition

// Wang-Ren Qiu 1, 2, 3 , Shi-Yu Jiang 2 , Zhao-Chun Xu 2 , Xuan Xiao 2, 3 and Kuo-Chen Chou 3, 4, 5 1 Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia, MO, USA 2 Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China 3 Gordon Life Science Institute, Boston, MA, USA 4 Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China 5 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia Correspondence to: Xuan Xiao, email: xxiao@gordonlifescience.org Keywords: RNA 5-methylcytosine sites, pseudo dinucleotide composition, physical-chemical property matrix, auto/cross-covariance, web-server Received: January 18, 2017      Accepted: March 15, 2017      Published: April 17, 2017 ABSTRACT Occurring at cytosine (C) of RNA, 5-methylcytosine (m 5 C) is an important post-transcriptional modification (PTCM). The modification plays significant roles in biological processes by regulating RNA metabolism in both eukaryotes and prokaryotes. It may also, however, cause cancers and other major diseases. Given an uncharacterized RNA sequence that contains many C residues, can we identify which one of them can be of m 5 C modification, and which one cannot? It is no doubt a crucial problem, particularly with the explosive growth of RNA sequences in the postgenomic age. Unfortunately, so far no user-friendly web-server whatsoever has been developed to address such a problem. To meet the increasingly high demand from most experimental scientists working in the area of drug development, we have developed a new predictor called iRNAm5C-PseDNC by incorporating ten types of physical-chemical properties into pseudo dinucleotide composition via the auto/cross-covariance approach. Rigorous jackknife tests show that its anticipated accuracy is quite high. For most experimental scientists’ convenience, a user-friendly web-server for the predictor has been provided at http://www.jci-bioinfo.cn/iRNAm5C-PseDNC along with a step-by-step user guide, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the approach presented here can also be used to deal with many other problems in genome analysis.