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.