5PSeq Explorer (RRID: SCR_027718): Interactive Analysis of Co-translational mRNA Decay and Ribosome Dynamics
Irene Stevens [ORCID: 0000-0003-3823-1499] 1,
Vicent Pelechano [ORCID: 0000-0002-9415-788X] 1
1 Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology (MTC),
Karolinska Institutet, Stockholm, Sweden
Background:
Co-translational mRNA decay occurs when 5′→3′ exonucleases follow the last translating ribosome, generating in vivo ribosome-protected fragments. Degradome sequencing (5PSeq) therefore offers unique insights into ribosome dynamics. Despite its potential, resources for systematic analysis of 5′P mRNA decay intermediates and associated features, such as ribosome stalls and collisions, are scarce.
Findings:
We introduce 5PSeq Explorer, a web-based platform built from 775 uniformly processed 5PSeq datasets across 23 species, enabling exploration of ribosome dynamics in vivo at codon, amino acid, and transcript levels.
Conclusions:
By integrating normalised counts, structured metadata, and scalable visualisation tools, 5PSeq Explorer provides a framework for studying the crosstalk between RNA decay and ribosome dynamics. To ensure reproducibility and accessibility, we offer both a public web interface and a Docker-based plug-and-play local version.
URL: https://fivepseq-explorer.serve.scilifelab.se/app/fivepseq-explorer
Raw count files for 775 samples, together with metadata and RNA composition, are available at:
5PSeq Explorer Data Freeze (Version 1)
Please cite:
Stevens, I. (2025). 5PSeq Explorer Data Freeze (Version 1) [Data set].
Karolinska Institutet.
https://doi.org/10.48723/zchv-5x22
The source code for the web version of 5PSeq Explorer is available at:
https://github.com/irenestevens8/5Pseq-Explorer/blob/main/web-app.R
For instructions on how to download and run precompiled versions of the software, please refer to the User Manual below.
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User Manual for 5PSeq Explorer:
5PSeq Explorer User Guide -
Docker Image for Web-version of 5PSeq Explorer:
https://hub.docker.com/repository/docker/stevensirene/fivepseq-explorer/tags/v1.3/sha256-24bb23231fd947c4574b2db344e0bcfb5726dbf6f504164dae80040a5cec5023 -
Docker Image for Local version 5PSeq Explorer:
https://hub.docker.com/repository/docker/stevensirene/5pseq-explorer-local/tags/v1.0/sha256-db7491fac8cbda52f9bdd6459cb2f178b4227c608370f5d7f464e0d77e61c87a
- Table S1: Public datasets used in this study
- Table S2: Metadata
- Table S3: RNA composition
For questions regarding data, code, and the web interface, please contact:
Irene Stevens
For questions regarding the 5PSeq method, please contact:
Vicente Pelechano