Abstract
Ribosome profiling (Ribo-Seq) is a technique that allows for the isolation and sequencing of mRNA fragments protected from nuclease digestion by actively translating ribosomes. Mapping these ribosome footprints to a genome or transcriptome generates quantitative information on translated regions. To provide access to publicly available ribosome profiling data in the context of transcriptomes we developed Trips-Viz (transcriptome-wide information on protein synthesis-visualized). Trips-Viz provides a large range of graphical tools for exploring global properties of translatomes and of individual transcripts. It enables analysis of aligned footprints to evaluate datasets quality, differential gene expression detection, visual identification of upstream ORFs and alternative proteoforms. Trips-Viz is available at https://trips.ucc.ie.
Highlights
Ribosome profiling [1], known as Ribo-Seq, is a technique that allows for large scale isolation of mRNA fragments that are being protected by actively translating ribosomes, see reviews [2,3,4,5,6,7,8]
SmProt [11] is another web based tool that aligns ribosome profiling data to the genomes of eight different organisms, combined with literature mining and mass spectrometry data it aims to find short translated ORFs and allows users to explore each of these data types extensively
The primary use of Trips-Viz is the interactive visualization of an aggregate of ribosome profiling data at subcodon resolution in the context of single transcripts, a feature not provided by other existing databases
Summary
Ribosome profiling [1], known as Ribo-Seq, is a technique that allows for large scale isolation of mRNA fragments that are being protected by actively translating ribosomes, see reviews [2,3,4,5,6,7,8] Sequencing these fragments, mapping them to a genome or transcriptome, and visualising these mappings can produce a global snapshot of which regions are being translated. RPFdb [12] permits visualisation of ribosome profiling data aligned to eight different organisms at a genomic level, as well as providing in depth information such as count tables, and meta-information such as the number of reads mapping to exonic/intronic/intergenic regions Unlike these genome based tools, RiboViz [13] provides data aligned to the Saccharomyces cerevisiae transcriptome. TranslatomeDb aligns Ribo-Seq data to the transcriptomes of 13 different organisms, along with RNASeq and RNC-Seq data [14]
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