Web-based visualization of coronavirus genomes and proteins

Project Summary: This supplemental proposal knits together several bioinformaticsvisualization tools in the service of SARS-CoV-2 genome analysis.The core of the proposal is a newly-prototyped JavaScript viewer,ABrowse, that is capable of rendering multiple sequence alignments,navigable by phylogenetic trees, and integrated with protein structureviews, all in a single embeddable component. The ABrowse viewer iscurrently employed to render the Pfam SARS-CoV-2 special release:a collection of 40 protein domains from the coronavirus genome, alongwith PDB structures. (ABrowse is also a candidate for Pfam's futuredefault viewer, as noted in the letters of support.)We propose to accelerate ABrowse development for use by theCOVID-19 pandemic, specifically targeting scaling, performance, andintegration issues that are most relevant to scientists studying thevirus. Chief amongst these is scaling ABrowse to handle millions ofprotein sequences (and/or SARS-CoV-2 genome sequences) bymeans of a new, compressed storage format suitable forrandom-access user-driven exploration of very large trees (andalignments) over the web.Beyond scaling, we also address integration, developing plugins forABrowse to run within JBrowse (the genome browser that is the focusof the project to which this is a supplemental proposal) as well asAuspice (the web dashboard of NextStrain, the phylogenetic genomealignment and annotation package that is widely used for COVID-19analysis). We also propose several user interface enhancements tomake ABrowse more useful as a navigation tool for COVID-19 data.