iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

Pengmian Feng; Hui Ding; Hui Yang; Wei Chen; Hao Lin; Kuo-Chen Chou

doi:10.1016/j.omtn.2017.03.006

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

Mol Ther Nucleic Acids. 2017 Jun 16:7:155-163. doi: 10.1016/j.omtn.2017.03.006. Epub 2017 Mar 29.

Authors

Pengmian Feng¹, Hui Ding², Hui Yang², Wei Chen³, Hao Lin⁴, Kuo-Chen Chou⁵

Affiliations

¹ Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, 063000, China.
² 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, 610054, China.
³ Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China; Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address: chenweiimu@gmail.com.
⁴ 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, 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address: hlin@uestc.edu.cn.
⁵ 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, 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address: kcchou@gordonlifescience.org.

Abstract

There are many different types of RNA modifications, which are essential for numerous biological processes. Knowledge about the occurrence sites of RNA modifications in its sequence is a key for in-depth understanding of their biological functions and mechanism. Unfortunately, it is both time-consuming and laborious to determine these sites purely by experiments alone. Although some computational methods were developed in this regard, each one could only be used to deal with some type of modification individually. To our knowledge, no method has thus far been developed that can identify the occurrence sites for several different types of RNA modifications with one seamless package or platform. To address such a challenge, a novel platform called "iRNA-PseColl" has been developed. It was formed by incorporating both the individual and collective features of the sequence elements into the general pseudo K-tuple nucleotide composition (PseKNC) of RNA via the chemicophysical properties and density distribution of its constituent nucleotides. Rigorous cross-validations have indicated that the anticipated success rates achieved by the proposed platform are quite high. To maximize the convenience for most experimental biologists, the platform's web-server has been provided at http://lin.uestc.edu.cn/server/iRNA-PseColl along with a step-by-step user guide that will allow users to easily achieve their desired results without the need to go through the mathematical details involved in this paper.

Keywords: PseKNC; RNA modification; SVM; collective effect; nucleotide chemicophysical property.