proteinbrowser

This page is a collection of resources for our "Proteins in the Genome Browser" paper published in the Journal of Molecular Biology. If you find this tool useful please cite our work

Diesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., & Holmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645

Screenshots

Main web server

• JBrowse 2 instances with 3-D protein structure and MSA plugins loaded. You can right-click any gene-of-interest to launch an MSA or 3-D protein viewer https://genomes.jbrowse.org

Other demos

• Ensembl Compara and TreeFam browser: This app provides a simple method to load data from Ensembl Compara Gene Trees and TreeFam into our app https://jbrowse.org/demos/msafam/
• Uniprot Browser: This app accesses the Uniprot API to get protein annotations https://cmdcolin.github.io/uniprot_browser

JBrowse 2 plugins

We created two independent JBrowse 2 plugins to help connect the genome browser to protein resources. Users can install these plugins via the in-app plugin store, or administrators can install the plugin for all their users:

• jbrowse-plugin-msaview - programmatically integrates react-msaview into JBrowse 2 for re-use, allows querying NCBI BLAST
• jbrowse-plugin-protein3d - programmatically integrates Mol* 3-D protein structure views, allows querying AlphaFoldDB and UniProt

User guide/developer guide for JBrowseMSA

A short user guide for JBrowseMSA is available here

https://github.com/GMOD/JBrowseMSA/blob/main/docs/user_guide.md

Live demos

• BRAF 3-D structure connected with genome - https://jbrowse.org/code/jb2/main/?config=%2Fucsc%2Fhg38%2Fconfig.json&session=share-oZc6gP5zSQ&password=zFvQi
• BRAF 1-D protein annotations view - https://jbrowse.org/code/jb2/main/?config=%2Fucsc%2Fhg38%2Fconfig.json&session=share-xgw4Y7Xoby&password=SMk7u
• BRAF V600 https://jbrowse.org/code/jb2/main/?config=%2Fucsc%2Fhg38%2Fconfig.json&session=share-muppi_-WsU&password=tvhMa

Footnote

Please feel free to contact us (https://jbrowse.org/jb2/contact) or make a github issue here if you have any questions or bug reports