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
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.
- 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.
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.
A short user guide for JBrowseMSA is available at https://github.com/GMOD/JBrowseMSA/blob/main/docs/user_guide.md
Please contact us or open a GitHub issue if you have any questions or bug reports.