Ribosome profiling (Ribo-seq), also known as ribosome footprinting, has revolutionized the ‘translatomics’ field by mapping the position of ribosome-protected fragments (RPFs), which typically range in length from 26 to 34 nucleotides (nt), over the entire transcriptome ( 1, 2). Thus, RiboToolkit will greatly facilitate the study of mRNA translation based on ribosome profiling. Besides, easy-to-use web interfaces were developed to facilitate data analysis and intuitively visualize results. Thus, we developed RiboToolkit ( ), a convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. Fortunately, the small size (26–34 nt) of ribosome protected fragments (RPFs) in Ribo-seq and the relatively small amount of sequencing data greatly facilitates the development of such a web platform, which is easy to manipulate for users with or without bioinformatic expertise. Although there are many existing tools to analyze Ribo-seq data, most of these tools are designed for specific or limited functionalities and an easy-to-use integrated tool to analyze Ribo-seq data is lacking.

However, analyzing and decoding translation information from Ribo-seq data is not trivial. Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under various physiological or experimental conditions.

Cds webtools