Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2

Colin Diesh; Garrett Stevens; Caroline Bridge; Gregory Hogue; Robert Buels; Scott Cain; Lincoln Stein; Ian Holmes

doi:10.1016/j.jmb.2026.169645

Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2

J Mol Biol. 2026 Jan 19:169645. doi: 10.1016/j.jmb.2026.169645. Online ahead of print.

Authors

Colin Diesh¹, Garrett Stevens², Caroline Bridge³, Gregory Hogue³, Robert Buels², Scott Cain³, Lincoln Stein³, Ian Holmes²

Affiliations

¹ University of California, Berkeley, Dept of Bioengineering, Berkeley, CA, USA. Electronic address: colindiesh@berkeley.edu.
² University of California, Berkeley, Dept of Bioengineering, Berkeley, CA, USA.
³ Ontario Institute for Cancer Research, Toronto, ON, Canada.

PMID: 41565000
DOI: 10.1016/j.jmb.2026.169645

Abstract

Recent advances in protein structure prediction have created high-confidence candidate structures for nearly every known protein-coding gene. At the same time, many software packages have been created to visualize protein structures, protein multiple sequence alignments (MSAs), and protein annotations. However, few software tools can highlight the direct relationship between nucleotide variation of protein-coding genes in genome space and the evolutionary and structural context of that variation in protein space. To help address these needs, we created a suite of robust and reusable JavaScript components to show protein structures, MSAs, phylogenies, and their relationship to protein-coding gene regions using the JBrowse 2 genome browser. This software allows users to interface with web services such as AlphaFoldDB and Foldseek to access pre-computed structures, or to upload protein structures from sources such as ColabFold or PDB. Our resources are available at https://github.com/GMOD/proteinbrowser.

Keywords: comparative genomics; data visualization; multiple sequence alignment; protein folding.