Unit

UNIT 12.16 Using the NONCODE Database Resource

  1. Li Xiyuan1,2,
  2. Bu Dechao1,3,
  3. Sun Liang4,5,6,
  4. Wu Yang4,
  5. Fang Shuangsang1,
  6. Li Hui1,
  7. Luo Haitao1,
  8. Luo Chunlong1,
  9. Fang Wenzheng1,
  10. Chen Runsheng7,
  11. Zhao Yi1,3

Published Online: 27 JUN 2017

DOI: 10.1002/cpbi.25

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

How to Cite

Xiyuan, L., Dechao, B., Liang, S., Yang, W., Shuangsang, F., Hui, L., … Yi, Z. (2017). Using the NONCODE database resource. Current Protocols in Bioinformatics, 58, 12.16.1–12.16.19. doi: 10.1002/cpbi.25

Author Information

  1. 1

    Institute of Computing Technology Chinese Academy of Sciences, Bioinformatics Research Group, Advanced Computing Research Laboratory, Beijing, China

  2. 2

    Beijing Zhongke Jingyun Technology Company Ltd., Medicine. Beijing, China

  3. 3

    Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Beijing, China

  4. 4

    Chinese Academy of Sciences, Institute of Computing Technology, Bioinformatics Research Group, Advanced Computing Research Laboratory, Beijing, China

  5. 5

    Beijing Zhongke Jingyun Technology Company Ltd., Bioinformatics, Beijing, China

  6. 6

    Wenzhou Medical University, College of Laboratory Medicine and Life Sciences, Department of Laboratory Medicine, Beijing, China

  7. 7

    Institute of Biophysics, Chinese Academy of Sciences, CAS Key Laboratory of RNA Biology, Beijing, China

Publication History

  1. Published Online: 27 JUN 2017
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Abstract

NONCODE is a comprehensive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNA genes), and thus NONCODE is essential to modern biological and medical research. Scientists are producing a flood of new data from which new lncRNA genes and lncRNA-disease relationships are continually being identified. NONCODE assimilates such information from a wide variety of sources including published articles, RNA-seq data, micro-array data and databases on genetic variation (dbSNP) and genome-wide associations (GWAS). NONCODE organizes all this information and makes it freely available to the public via the Internet. The NONCODE protocol provides step-by-step instructions on how to browse and search lncRNA information such as sequence, expression, and disease relationships, how to use the tools for functional prediction, species conservation assays, blast analysis, identifier conversion, and, finally, how to submit sequences to identify lncRNA genes. As of Dec 2016, NONCODE has cataloged 487,851 lncRNA genes sequenced from 16 species. © 2017 by John Wiley & Sons, Inc.

Keywords:

  • long non-coding RNA;
  • NONCODE database;
  • information retrieval;
  • species conservation;
  • bioinformatics;
  • functional annotation
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