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  • deepBase: a database for annotating and discovering ncRNAs from deep sequencing data

    Dear All,

    We introduce a novel platform/database, deepBase, which we have developed to map, store, retrieve, annotate, integrate and visualize deep sequencing-derived small RNAs, and facilitate transcriptomic research and the discovery of novel ncRNAs.

    deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 2010,38: D123-D130. December 4, 2009.

    deepBase is available at:

    Features of deepBase as follows,
    Deep sequencing data and species
    Deep sequencing data from 185 (now is 237) small RNA libraries from diverse tissues and cell lines.
    Seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana.
    Annotation and identification of diverse small RNAs
    we annotated and identified
    ~380 000 unique ncRNA-associated small RNAs (nasRNAs)
    ~1.5 million unique promoter-associated small RNAs (pasRNAs)
    ~4.0 million unique exon-associated small RNAs (easRNAs)
    ~6 million unique repeat-associated small RNAs (rasRNAs)
    Discovering RNA clusters and long ncRNAs
    We identified
    about 1.2 million RNA clusters that include multiple classes of infrastructural ncRNAs (e.g. tRNAs, rRNAs, snRNA and snoRNAs), miRNAs precursor, piRNA precursors, repeat-associated siRNA precursors and evolutionarily conserved phastCons elements.
    ~2000 microRNA candidates were identified from deep sequencing data using modified miRDeep program.
    ~1890 snoRNA candidates were predicted from RNA clusters using our snoSeeker program.
    A new visualization tool, deepView genome browser, to provide an integrated view of mapped reads, known and predicted ncRNAs, protein-coding genes and RNA clusters and their expression peaks (mapped small RNA density).
    Stand-alone graphical interface (GUI) tools
    Stand-alone graphical user interface (GUI) tools for deep sequencing-derived small RNA were provided in deepBase. All these softwares are preliminary version. We are actively updating and maintaining them.

    This is the first version of deepBase database. We look forward to your feedback.

    Last edited by yjhua2110; 11-04-2010, 04:41 AM.

  • #2
    We are integrating published next-generation small RNA-Seq datasets to our deepBase data. And we hope you contribute your next-generation small RNA-Seq datasets to our deepBase.

    For more information see the deepBase submission page

    Thank you very much!


    • #3
      mapped reads associated with known microRNAs

      We also have mapped reads from deep-sequencing experiments to known microRNAs downloaded from miRBase and developed a variety of interfaces and graphical visualization to view these mapped reads. You can retrieve a list of microRNAs and list of variants and their read counts and isomiRs...

      Web interfaces to view mapped reads associated with known microRNAs as follows:
      Last edited by yjhua2110; 11-04-2010, 04:51 AM.


      • #4
        heatmap (microRNA and ncRNA expression pattern)

        We have updated the heatmap (microRNA and ncRNA expression pattern) generated from mapped deep-sequencing reads.

        web interface to view heatmap as follows:

        Last edited by yjhua2110; 11-04-2010, 04:51 AM.


        • #5
          snoSeekerNGS: Discovering snoRNAs from pooled deep-sequencing data

          We had released a software package, snoSeekerNGS, for discovering snoRNAs from pooled deep sequencing data.

          SnoSeekerNGS is freely available from the following URL: Choose the appropriate platform for a binary distribution or a graphical user interface (GUI) distribution.
          Last edited by yjhua2110; 11-30-2010, 12:15 AM.


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