Associate Professor, Biochemistry/Microbiology Department
Phone: (250) 721-6507
Research area: virology, poxvirus virulence factors, bioinformatics
Not that long ago, it was rare for a virologist to have the complete genomic sequence of their object of study; now virologists are starting to compare genomes of individual viruses among the same species. In fact, sequencing technology has evolved so fast, researchers are often inundated with too much sequence data.
The need for increasingly complex databases and software to organize and analyze genomic data is what drew Dr. Chris Upton, a poxvirus expert, to the field of bioinformatics. Working with collaborators at the University of Alabama at Birmingham, Upton’s lab has developed a viral genome database with an interface specifically designed for virologists. The database and associated software tools are available free at the Viral Bioinformatics Resource Center, one of eight bioinformatics resource centres funded by the U.S. National Institute of Health.
The Viral Bioinformatics Resource Center started with a database for poxviruses. It then expanded to eight other virus families, starting with emerging infectious agents, such as the Ebola virus and hanta virus. The two most recent additions are hepatitis C virus and dengue virus.
In Upton’s lab, computer scientists work alongside virologists: half of Upton’s grad students are cross-appointed in UVic’s computer science department. The center offers a variety of software tools. The main one, called VOCs (Viral Orthologous Clusters), allows users to search the database by several criteria related to genome, gene, or protein family. Other tools allow you to view or edit gene annotations, such as regulatory sequences, gene names and start/stop codons.
Virologists use the database and tools for countless projects. Often researchers want to glean insight into a gene’s function by grouping their gene into an orthologous group ( a group of genes that share an ancestral origin and have diverged through speciation). Upton has done this with his own research on poxviruses, identifying several poxvirus virulence factors.
Others are looking at evolution. For instance, Upton is working with Dr. Delano James at the Canadian Food Inspection Agency’s Centre for Plant Health to study the evolution of fruit tree viruses that affect cherry, plum and peach crops. Others are looking for the evidence of viral genes that have been incorporated into the genomes of host organisms.
In the case of dengue fever, researchers are comparing genomes of dengue virus collected from different disease epicenters, to track how the virus changes and how it has spread, based on sequence similarities.
The role of bioinformatics is only going to increase in the next couple of years. When Upton is asked to predict the next big thing in bioinformatics, he points to protein structures. Right now, deciphering a protein structure through protein crystallography is still labourious and often unsuccessful. But if that changes, there will be another explosion of data (some are calling it structuromics) requiring a new set of bioinformatics tools to organize it. Should Upton’s team of virologists and computer scientists get tired of genomes, they will be well set to take on structuromes.