deepBase is a platform for annotating and discovering small (microRNAs, siRNAs, piRNAs...), long ncRNAs (lncRNAs) and circular RNAs (circRNAs) from next generation sequencing data. deepBase v2.0 provides a set of useful tools to decode evolution and expression patterns of diverse ncRNAs across 19 species from 5 clades and to infer their functions. We provide accurate annotations of lncRNAs from RNA-seq experiements. By combining expression profiles of protein-coding genes and functional genomic annotations, we predict the function of lncRNAs from co-expression networks derived from RNA-Seq data. deepBase v2.0 also provided an integrative, interactive and versatile web graphical interface to display multidimensional data, and facilitate transcriptomic research and the discovery of novel ncRNAs.

The workflow of deepBase v2.0

How to cite:

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.

Ling-Ling Zheng, Jun-Hao Li, Jie Wu, Wen-Ju Sun, Shun Liu, Ze-lin Wang, Hui Zhou, Jian-Hua Yang and Liang-Hu Qu. deepBase v2.0: Identification, Expression, Evolution and Function of Small RNAs, LncRNAs and Circular RNAs from Deep-sequencing Data. has been submitted to NAR.