About the deepBase Site

Welcome to deepBase

      deepBase, a platform for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from next generation sequencing data. deepBase allows the mapping, storage, retrieval, analysis, integration, annotation, mining and visualization of next generation sequencing data from different technological platforms, tissues and cell lines of different organisms. deepBase also provided an integrative, interactive and versatile web graphical interface to display multidimensional data, and facilitate transcriptomic research and the discovery of novel ncRNAs.   >>Tutorial

How to cite:

    If you make use of the data presented here, please cite the following article in addition to the primary data sources:
   Jian-Hua Yang, Peng Shao, Hui Zhou, Yue-Qin Chen, and Liang-Hu Qu.
   deepBase: a database for deeply annotating and mining deep sequencing data.
   Nucleic Acids Res. 2010 Jan;38(Database issue):D123-D130. Epub 2009 Dec 4.
   [Full Text]   [Print PDF]   [Screen PDF]   [Supplementary Data]

      If you interested in long noncoding RNAs(lncRNAs, lincRNAs) microRNAs, snoRNAs and circRNAs, we think you also interested in our novel deepBase V2.0 platform, which we have developed to decode Identification, Expression, Evolution and Function of Small RNAs (snoRNAs, miRNAs, tRNAs, snRNAs etc.), LncRNAs and Circular RNAs from small and long RNA sequencing Data.   

The distinctive features of deepBase         Release 1.2: 2010


  • snoSeekerNGS: discovering snoRNAs from pooled deep-sequencing data.
  • >370 million sequence reads from 237 small RNA libraries
  • Seven model organisms: range from plant to mammal(human)
  • >380,000 unique nasRNAs originating from known ncRNAs
  • ~1.5 million unique promoter-associated small RNAs (pasRNAs)
  • ~4.0 million unique exon-associated small RNAs (easRNAs)
  • ~6.0 million unique repeat-associated small RNAs (rasRNAs)
  • ~1.2 million RNA clusters for discovering novel ncRNAs
  • >2000 microRNA candidates prediected by miRDeep
  • deepTools: Graphical tools for deep-sequencing data
      Submit Your Data      More information  >>


deepBase database is curated by JianHua Yang.
For comments, suggestions on the deepBase database, please use the E-mail: yjhua2110@yahoo.com.cn
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