Software and Resource

Provides access to our analysis of mRNA expression in several RNA-Seq datasets of zebrafish embryos.

Provides access to our single-cell RNA metabolic labeling data and analysis of mRNA transcription and degradation dynamics during cell-type specification in zebrafish embryos

UTR-Seq is a Matlab package for the analysis of massively parallel reporter assays (MPRA) of RNA stability, in order to identify short sequence elements that regulate the stability of RNA transcripts. The resulting model can then apply to any input sequence of choice.

DRiLL is a computational approach that (1) quantifies the level of each precursor and mature RNA at splicing junction resolution from RNA-seq data, and (2) determines its transcription, processing and degradation rates by also combining RNA metabolic labeling data. 

In the RNA life cycle portal you can download the DRiLL software to apply to your own data, download our own data for a high-resolution temporal map of rRNA-depleted and 4sU-labeled RNA in mouse immune dendritic cells responding to LPS, or search any mouse transcript for its precursor and mature RNA levels and transcription, processing and degradation rates in the dendritic cells response.

RNApromo is an efficient computational tool, based on probabilistic graphical models, for identifying shared structural elements within mRNA sequences. RNApromo predicts structural motifs that are common to a set of input RNA sequences, including information on both the RNA sequence and its structure.