Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

Abstract Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a serv...

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Bibliographic Details
Published in:Nucleic acids research 2021-07, Vol.49 (W1), p.W662-W670
Main Authors: Kiniry, Stephen J, Judge, Ciara E, Michel, Audrey M, Baranov, Pavel V
Format: Article
Language:English
Subjects:
Mass Spectrometry
Open Reading Frames
Protein Biosynthesis
Proteomics
Ribosomes - metabolism
RNA-Seq
Sequence Analysis, RNA - methods
Software
Web Server Issue
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Summary:Abstract Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server functionality of Trips-viz which also has been greatly improved. Trips-viz now enables visualisation of proteomics data from a large number of processed mass spectrometry datasets. It can be used to support translation inferred from Ribo-Seq data. Users are now able to upload a custom reference transcriptome as well as data types other than Ribo-Seq/RNA-Seq. Incorporating custom data has been streamlined with RiboGalaxy (https://ribogalaxy.ucc.ie/) integration. The other new functionality is the rapid detection of translated open reading frames (ORFs) through a simple easy to use interface. The analysis of differential expression has been also improved via integration of DESeq2 and Anota2seq in addition to a number of other improvements of existing Trips-viz features. Graphical Abstract Graphical Abstract Trips-Viz enables numerous analyses of public and user-generated ribosome profiling and proteomics data.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkab323