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

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.