Chris Lewis, Steve Karcz, Andrew Sharpe, Isobel Parkin
We have developed an interactive, browser-based SVG application for the visualization and mining of genome data from the model plant Arabidopsis thaliana. The genome of this plant consists of DNA sequence information organized into five chromosomes that can be up to 30 million base pairs in length and contain up to 7000 distinct genes distributed along each chromosome. This linear arrangement makes the data particularly amenable to display using SVG as it provides a spatial relationship between the constituent parts of the genome. It is important that the user can scale from an overview encompassing millions of base pairs to a detailed view of a specific region without losing spatial reference as the user will often only be interested in a small part of the whole. For instance, each gene has a specific structure that can only be visualized at high levels of magnification. Additionally, client-side scripting allows the user to create new views, or to request supplemental data which can be loaded and dismissed on demand.
SVG has allowed us to create a visually appealing, functional browser for our data. The CGUI library is our attempt at a generic SVG based GUI library, and demonstrates that such a library is completely feasible. While we used CGUI to display genomics data, it seems that such a library could be useful for other web developers who need to display a large dataset in an organized manner. Inquiries about the CGUI library may be directed to lewisCT@em.agr.ca.
Molecular Genetics Section
Running Title: SVG based genome viewer