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Old 12-15-2009, 11:18 PM   #1
Location: China

Join Date: Dec 2009
Posts: 43
Default deepBase: annotating and discovering small and long RNAs from deep sequencing data

Dear All,

We describe a novel 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 is available at:

deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res.,2010,38:123-D130.December 4, 2009.

Features of deepBase as follows,
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, 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.
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).

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


Last edited by rnaNGS; 12-23-2009 at 03:59 AM.
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Old 01-03-2010, 06:22 AM   #2
Location: china

Join Date: Nov 2009
Posts: 67

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!
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