Introduction

RPFdb is a publicly accessible repository dedicated to hosting, analyzing, and visualizing ribosome profiling (Ribo-seq) data. The latest version, RPFdb v3, offers an expansive dataset featuring Ribo-seq data from 5,018 samples across 496 studies, complemented by matched RNA-seq data from 2,343 samples, encompassing 34 distinct species. The contexts are organized into distinct levels: 1) Study Level: This level provides a meta-information for each study along with a convenient search button. 2) Sample Level: Users gain a global perspective on translated mRNA within each sample, along with a list of the most highly translated mRNA of each study sample. 3) Gene Level: Here, normalized counts of translated mRNA across different genomic location of a gene are presented, aggregated from multiple samples and studies. 4) Translational efficiency Level: a measure of how effectively mRNA molecules are translated into proteins is achieved by comparing mRNA abundance (from RNA-seq) with ribosome occupancy (from Ribo-seq) for individual genes. To facilitate exploration of the wealth of information within RPFdb, a genome browser is available for querying and visualizing context-specific translated mRNA. Beyond quantitative data and intuitive visualizations pertaining to mRNA translation, RPFdb also supplies annotation details regarding actively translated open reading frames(ORFs) and pause scores of tripeptide motifs.