Ribosome profiling (Ribo-seq) has revolutionized the translatomics field by mapping the position of ribosome-protected fragments (RPFs), which is typically ranging from 26bp to 34bp, over the entire transcriptome. The scientific community has employed Ribo-seq to answer a wide range of questions, ranging from the identification of translated small open reading frames to the quantification of translational process, while gaining precious mechanistic insights on RNA translation process itself. Although there are already many tools were developed to analysis Ribo-Seq data, such as riboORF, ORF-RATER, RpBp, PreTIS and RiboCode for ORF identification, Riborex, SPECtre, RiboDiff and RiboTools for differential translation analysis, they are all designed for specific or limited functions. There is still lacking an integrated tool to analysis RNA translation in an integrated way. The research community has high demand for such a one stop tool to help them analysis the Ribo-Seq data. Consider the relative small size of RPFs and relative small amount of sequencing data, the development of a web server, which is very easily for uses to use, is feasible. Here, RiboToolkit, an integrated web server, is developed for Ribo-seq data analysis.

RiboToolkit, a freely available web-based service, has these main features:

• RNA translation can be studied for as many as 40 species
• Easily Ribo-seq data quality control and quality evaluation
• Unbiased analyze gene translation efficiency and gene differential translation
• Codon usage analyses to identify highly active codons and codon stalling events
• Actively translated ORF identification with higher speed and specificity
• Meta-gene analysis of RPFs on CDS region to show translation velocity distribution for entire translation cycle
• Various gene function annotations for genes showing differential translation
• Different ways of data uploading are supported
• Very user-friendly web interfaces and convenient data analysis queue system

RiboToolkit grants free access for every user.

RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode RNA translation at codon resolution

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