RPFdb is a public resource for hosting, analyzing and visualizing ribosome profiling (Ribo-seq) data. The latest version, RPFdb v2.0 beta (20200101), contains Ribo-seq data from 3,603 samples and matched RNA-seq data from 1,962 samples comprising 372 studies covering 33 different species, processed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. 1) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; 2) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; 3) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore the rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. In addition to providing quantitative information and intuitive visualization-oriented information about gene translation, RPFdb v2.0 beta also provides annotation information and translational efficiency (TE) about actively translated open reading frames(ORFs).

  • Get RPFdb data
    Downloads for the latest version (currently: V2.0 beta) of the datasets

  • Release Notes
    [2022-01-01] RPFdb Version 2 beta.
    [2018-06-01] RPFdb Version 2.
    [2015-07-04] RPFdb Version 1.