Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

Nucleic Acids Research
Stephen J KiniryPavel V Baranov

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.

References

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Citations

Mar 17, 2019·International Journal of Molecular Sciences·Gesche K GerresheimMichael Niepmann
Nov 25, 2019·Wiley Interdisciplinary Reviews. RNA·Stephen J KiniryPavel V Baranov
Sep 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Gary LoughranDmitry E Andreev
Jul 25, 2019·Nature Protocols·Carla V GalmozziGünter Kramer
Jun 4, 2020·Computational and Structural Biotechnology Journal·Tulio L CamposNeil D Young
Aug 24, 2019·Journal of Molecular Biology·Janinah BaclaocosJohn F Atkins
Mar 29, 2021·The Journal of Biological Chemistry·Géssica C BarrosFernando L Palhano
May 1, 2021·International Journal of Molecular Sciences·Alexander V GopanenkoGalina G Karpova
May 6, 2021·Nucleic Acids Research·Stephen J KiniryPavel V Baranov
Jun 27, 2021·Human Mutation·Alexandra Y FilatovaMikhail Y Skoblov
Aug 28, 2021·International Journal of Molecular Sciences·Daria KoninaMikhail Skoblov
Sep 8, 2021·Frontiers in Cell and Developmental Biology·Oza ZaheedKellie Dean

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Methods Mentioned

BETA
Ribo-Seq
RNA-Seq

Software Mentioned

Trips
Bowtie
Viz
db
SmProt
TranslatomeDb
RiboViz
RPF
Chrome
Firefox

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