The Genome Explorer Genome Browser

Abstract

Are two adjacent genes in the same operon? What is the order and spacing between several transcription-factor binding sites? Genome browsers are software data-visualization and exploration tools that enable biologists to answer questions such as these. In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user’s web browser and dynamically generating visualizations locally, we enable fine control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have high information density that provides larger amounts of genome context and sequence information to be presented in a given sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for analysis of large-scale datasets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming.