Genome Context Viewer: A User-Friendly Web Application for Visualizing and Mining Shared Gene Content Among Multiple Genomes

Advances in sequencing technology and in corresponding algorithms for genome assembly and gene annotation have led to the availability of an ever-increasing number of annotated whole genome assemblies. These vary widely in terms of the technologies and algorithms used in their production, the quality of representation and the complexity of the genomes targeted, as well as the magnitude of the evolutionary distances traversed when comparing among them. For many comparative questions, users of these resources are less concerned with sequence level details than with basic questions surrounding functional content and the genomic contexts in which it occurs. The Genome Context Viewer (GCV) is an open source web-based tool that allows users to search, align, and visualize multiple regions of genomes using simplified representation of their total information content. By handling ordered sequences of gene family memberships as a unit of search and comparison, the user interface enables quick and intuitive assessment within syntenic contexts of the degree of gene content conservation or divergence, copy number changes, and various types of structural events. Microsyntenic blocks computed on the fly can be further augmented by chromosome scale synteny tracks and pairwise dot-plots, which indicate the size and structure of content and structural variation “at a glance”. The service-oriented design of the client allows genome content to be aggregated from multiple sources, thus enabling the user to make comparisons among genomes hosted independently. A live version of the tool will be available during the poster session.

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