proteinbrowser - Resources for visualizing 3-D protein structures and multiple sequence alignments using JBrowse 2

This page is a collection of resources for our paper "Proteins in the Genome Browser" (in prep)

Screenshots

Web server resources

• JBrowse 2 instances with protein plugins loaded. You can right-click any gene-of-interest to launch an MSA or 3-D protein viewer https://jbrowse.org/demos/app/
• React-msaview standalone app. This app demonstrates our MSA viewer functionality (no JBrowse 2 integration) https://gmod.org/react-msaview/
• 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

Software resources

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 the react-msaview

A short user guide for react-msaview is available here

https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md

Live demos

• BRAF 3-D structure connected with genome - https://jbrowse.org/demos/app/?session=share-SyUYMmF2R3&password=0ycYQ
• BRAF multiple sequence alignment connected with genome - https://jbrowse.org/demos/app/?session=share-IUdmod8VB7&password=MKfuU
• BRAF 1-D protein annotations view - https://jbrowse.org/demos/app/?session=share-YYu64eFQ3U&password=sDims