Abstract
Context Long, translation was thought as a stable and uniform process by which a ribosome produces a protein encoded by the main Open Reading Frame (ORF) of an mRNA. Recently, growing evidence support uncom-plete correlation between RNA and protein levels, the existence of alternative ORFs in numerous mammalian RNAs, and ribosomes' implication in gene expression regulation, thereby challenging previous views of translation. Ribosome profiling (aka Ribo-seq) has revolutionized translation study by enabling the mapping of translating ribosomes on the whole transcriptome using deep-sequencing. Motivation Despite increasing use of Ribo-seq, recent review articles prompt that flexible, interactive tools for mining such data are missing. As Ribo-seq protocols still evolve, flexibility is highly desirable for the end-user. Result: Here we describe RNA-Ribo-Explorer (RRE) a stand-alone tool that fills this gap. With RRE, one can explore read-count profiles of the transcriptome obtained after mapping, compare them in many conditions, and visualize the profiles of individual RNAs. Importantly, one can interrogate datasets using queries combining several numerical criteria to detect interesting subsets of RNAs. This feature seems useful for finding candidate RNAs whose translation status or processing has changed across conditions. Availability RRE is written in Java and can be used on Linux, Mac or Windows platforms; it comes with a manual and is freely available at https://gite.lirmm.fr/rivals/RRE/-/releases .