SyntenyVista

Visualization of genome comparisons is an important research tool in biology, medicine and agricultural research. We present a new visualization system, SyntenyVista, which allows for interactive exploration of genome comparisons. It incorporates a novel feature called cartoon scaling designed to improve the user's ability to understand gene relationships. SyntenyVista is being deployed in the context of e-Science where it will provide an entry point to integrated data on genomes, animal models of disease, and disease genes

VisGenome: visualization of single and comparative genome representations

VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser

Genome visualisation and user studies in biologist-computer interaction

We surveyed a number of genome visualisation tools used in biomedical research. We recognised that none of the tools shows all the relevant data geneticists who look for candidate disease genes would like to see. The biological researchers we collaborate with would like to view integrated data from a variety of sources and be able to see both data overviews and details. In response to this need, we developed a new visualisation tool, VisGenome, which allows the users to add their own data or data downloaded from other sources, such as Ensembl. VisGenome visualises single and comparative representations of the rat, the mouse, and the human chromosomes, and can easily be used for other genomes. In the context of VisGenome development we made the following research contributions. We developed a new algorithm (CartoonPlus) which allows the users to see different kinds of data in cartoon scaling depending on a selected basis. Also, two user studies were conducted: an initial quantitative user study and a mixed paradigm user study. The first study showed that neither Ensembl nor VisGenome fulfil all user requirements and can be regarded as user-friendly, as the users make a significant number of mistakes during data navigation. To help users navigate their data easily, we improved existing visualisation techniques in VisGenome and added a new technique CartoonPlus. To verify if this solution was useful, we conducted a second user study. We saw that the users became more familiar with the tool, and found new ways to use the application on its own and in connection with other tools. They frequently used CartoonPlus, which allowed them to see small regions of their data in a way that was not possible before

VisGenome: visualization of single and comparative genome representations

Summary: VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser. Availability: http://www.dcs.gla.ac.uk/~asia/VisGenome Contact: [email protected]

The visual language of synteny

The study of polygenic disorders such as cardiovascular and metabolic diseases requires access to vast amounts of experimental and in silico data. Where animal models of disease are being used, visualization of syntenic genome regions is one of the most important tools supporting data analysis. We define what is required to visualize synteny in terms of the data being displayed, the screen layout, and user interaction. We then describe a prototype visualization tool, SyntenyVista, which provides integrated access to quantitative trait loci, microarray, and gene datasets. We believe that SyntenyVista is a significant step towards an improved representation of comparative genomics data