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Chen W, Tang H, Ye J, et al. iRNA-PseU: Identifying RNA pseudouridine sites. Mol Ther Nucleic Acids. 2016;5:e332doi: 10.1038/mtna.2016.37.
Chen, W., Tang, H., Ye, J., Lin, H., & Chou, K. C. (2016). iRNA-PseU: Identifying RNA pseudouridine sites. Molecular therapy. Nucleic acids, 5e332. https://doi.org/10.1038/mtna.2016.37
Chen, Wei, et al. "iRNA-PseU: Identifying RNA pseudouridine sites." Molecular therapy. Nucleic acids vol. 5 (2016): e332. doi: https://doi.org/10.1038/mtna.2016.37
Chen W, Tang H, Ye J, Lin H, Chou KC. iRNA-PseU: Identifying RNA pseudouridine sites. Mol Ther Nucleic Acids. 2016;5:e332. doi: 10.1038/mtna.2016.37. PMID: 28427142; PMCID: PMC5330936.
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Mol Ther Nucleic Acids. 2016;5:e332. doi: 10.1038/mtna.2016.37.

iRNA-PseU: Identifying RNA pseudouridine sites.

Molecular therapy. Nucleic acids

Wei Chen, Hua Tang, Jing Ye, Hao Lin, Kuo-Chen Chou

Affiliations

  1. Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China; Gordon Life Science Institute, Boston, Massachusetts, USA. Electronic address: [email protected].
  2. Department of Pathophysiology, Southwest Medical University, Luzhou, China.
  3. Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.
  4. Gordon Life Science Institute, Boston, Massachusetts, USA; Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China. Electronic address: [email protected].
  5. Gordon Life Science Institute, Boston, Massachusetts, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia. Electronic address: [email protected].

PMID: 28427142 PMCID: PMC5330936 DOI: 10.1038/mtna.2016.37

Abstract

As the most abundant RNA modification, pseudouridine plays important roles in many biological processes. Occurring at the uridine site and catalyzed by pseudouridine synthase, the modification has been observed in nearly all kinds of RNA, including transfer RNA, messenger RNA, small nuclear or nucleolar RNA, and ribosomal RNA. Accordingly, its importance to basic research and drug development is self-evident. Despite some experimental technologies have been developed to detect the pseudouridine sites, they are both time-consuming and expensive. Facing the explosive growth of RNA sequences in the postgenomic age, we are challenged to address the problem by computational approaches: For an uncharacterized RNA sequence, can we predict which of its uridine sites can be modified as pseudouridine and which ones cannot? Here a predictor called "iRNA-PseU" was proposed by incorporating the chemical properties of nucleotides and their occurrence frequency density distributions into the general form of pseudo nucleotide composition (PseKNC). It has been demonstrated via the rigorous jackknife test, independent dataset test, and practical genome-wide analysis that the proposed predictor remarkably outperforms its counterpart. For the convenience of most experimental scientists, the web-server for iRNA-PseU was established at http://lin.uestc.edu.cn/server/iRNA-PseU, by which users can easily get their desired results without the need to go through the mathematical details.

Copyright © 2016 Official journal of the American Society of Gene & Cell Therapy. Published by Elsevier Inc. All rights reserved.

Keywords: Web-server; iRNA-PseU; nucleotide chemical property; nucleotide frequency; pseudouridine; Ψ site

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