deepBase: annotating and discovering small and long RNAs from deep sequencing data

[rnaNGS]

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: http://deepbase.sysu.edu.cn/

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

http://nar.oxfordjournals.org/cgi/content/full/gkp943

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.
Visualization
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.

Thanks!

[yjhua2110]

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:

http://deepbase.sysu.edu.cn/submit.php

Thank you very much!