CCG, Catalogue of Cancer Genes/lncRNAs, is an assembly resource of coding and noncoding genes associated with cancer. In addition, drug-gene information in CCG provides a useful guide to the development of new anti-cancer drugs.
RNAfeature provides a common set of conserved features for ncRNAs across multiple species. The models in RNAfeature were trained on canonical ncRNAs (e.g.,tRNAs,rRNAs, miRNAs, snRNAs, snoRNAs, 7SK RNAs, Y RNAs).
COME is a tool to calculate COding potential from Multiple fEatures for a given transcript. The models in COME were trained on mRNAs and long ncRNAs (lncRNAs).
An app to for processing RNA-seq data, identify and characterize known and novel transcripts, including protein coding genes and noncoding RNAs.
RME is a tool for RNA secondary structure prediction with multiple types of experimental probing data. It is based on the RNAstructure package. It also provides preprocessing scripts for transforming the SHAPE, PARS and DMS-seq data into pairing probability according a posterior probabilistic model. Moreover, it also contains a utility for optimizing the parameters of RME by RME-Optimize.
RNAex is an RNA secondary structure prediction server enhanced by high-throughput experimental data. We have re-mapped raw data of the published probing experiments to the whole genome, thus users can predict secondary structures for novel RNA transcripts.
CLIPdb is an integrative resource of CLIP-seq studies. It aims to characterize the regulatory networks between RNA binding proteins (RBPs) and various RNA transcript classes by integrating large amounts of CLIP-seq (including HITS-CLIP, PAR-CLIP and iCLIP as variantions) data sets.
POSTAR (CLIPdb 2) is a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. It enables the experimental biologists to connect protein-RNA interactions with multi-layer information of post-transcriptional regulation and functional genes, and helps them generate novel hypotheses about the post-regulatory mechanisms of phenotypes and diseases.