JBrowse within the Arabidopsis Information Portal

The Arabidopsis Information Portal (https://www.araport.org, Araport) is an NSF and BBSRC funded project aimed at providing an interface for users to access a wide variety of Arabidopsis data by leveraging powerful web services. One of the aspects of our portal is to expose data visualization capabilities to the Arabidopsis research community by implementing JBrowse (https://apps.araport.org/jbrowse/?data=arabidopsis) and making novel extensions to support specific use-cases. To this end, we integrated datasets both from local and remotely retrieved sources like the EPIC-CoGe project using RESTful web services. To support these diverse sets of tracks, we developed the “ComboTrackSelector”, a JBrowse plugin, which allows the coexistence of Hierarchical and Faceted track selectors. This enables the capability to partition tracks, placing metadata rich tracks in the “Faceted” selector while using the default “Hierarchical” selector for everything else. In response to user requests for a TAIR SeqViewer-like capability, we built a dynamic sequence viewer add-on, “SeqLighter”, using the BioJS framework (http://biojs.net/). This can be configured as a hook to any “Gene Model” track via the right-click context menu and offerend-users with the capability to view the genomic sequence underlying the gene models (genic regions plus customizable flanking regions), highlight sub-features (like UTRs, exons, introns, start/stop codons) and export the annotated output in various formats (SVG, PNG, JPEG).