Gene-RiViT: A visualization tool for comparative analysis of gene neighborhoods in prokaryotes

The genomes of prokaryotes are dynamic and shuffling of gene order occurs frequently, along with horizontal transfer of genes from external sources. Local conservation of gene order tends to reflect functional constraints on the genome or on a biochemical subsystem. Comparison of the local gene neighborhoods surrounding a gene of interest gives insight into evolutionary history and functional potential of the gene. The Genomic Ring Visualization Tool (Gene-RiViT) is a high speed, intuitive visualization tool for investigating sequence environments of conserved genes among related genomes. Gene-RiViT allows the user to interact with interconnected global and local visualizations of gene neighborhoods and gene order, through a web-based interface that is easily accessible in any browser. The primary visualization is a wheel of nested rotating circles, each of which represents a single genome. This visualization is similar to common circular genome alignment views, except that the rings can be realigned with each other dynamically based on user selections within the ring view or one of the coordinated views. By allowing the user to dynamically realign genomes and focus on a locally conserved region of interest, and using or-thology connections to highlight corresponding structures among genomes, this view provides insight into gene context and preservation of neighbor relationships as genomes evolve. Visualizations are linked into a coordinated multiple view interface to provide multiple selection methods and entry points into the data. These approaches make Gene-RiViT a flexible, unique tool for examining gene neighborhoods that improves on existing methods.