proteinbrowser

A collection of resources for our paper "Proteins in the Genome Browser," published in the Journal of Molecular Biology.

If you find these tools 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

Featured demo

The JBrowseMSA Gene Explorer auto-launches a linked view combining a multiple sequence alignment (MSA), a 3-D protein structure, and a linear genome view — the graphical abstract of our paper.

Screenshots

Other ways to access the protein browser

• genomes.jbrowse.org — JBrowse 2 instances with the 3-D protein structure and MSA plugins loaded. Right-click any gene of interest to launch an MSA or 3-D protein viewer.
• Ensembl Compara and TreeFam browser — load data from Ensembl Compara Gene Trees and TreeFam.
• Uniprot Browser — accesses the UniProt API to retrieve protein annotations.

JBrowse 2 plugins

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

• jbrowse-plugin-msaview — integrates react-msaview into JBrowse 2 and supports querying NCBI BLAST.
• jbrowse-plugin-protein3d — integrates Mol* 3-D protein structure views and supports querying AlphaFold DB and UniProt.

User and developer guide

User guide and developer docs for JBrowseMSA are available at https://gmod.org/JBrowseMSA/

Contact

Please contact us or open a GitHub issue if you have any questions or bug reports.