2004-2005 Seminar Series

Our work has explored the potential of structural variables for studies in comparative genomics. We begin with a very simple variable of this type: the identification of identical nucleotide segments. Exact match between substrings is often implemented using suffix trees; indeed Delcher et al. (1999) have implemented a program (MUMmer) for aligning whole genomes based on exact match substrings.

A comparison of Neisseria meningitidis strains Z2491 and MC58 has confirmed the expected similarity between the genomes. Dot plots served as a simple and effective presentation method. We observed a number of sizeable direct-complementary matches, in the region below about 700 kbp and at ~2mbp's. Only small direct-direct matches were observed. Published observations about these two strains can be interpreted in light of such simple conclusions. For example, IHT's (islands of horizontally transferred DNA) and Pai's (pathogenicity islands) have been identified in the literature and they are related to the identified transpositions, simple insertions, and polymorphic regions.

Neisseria meningitidis is characterized by five pathogenic serogroups. Serogroup A is responsible for the major epidemics and pandemics of meningococcal disease in Africa and China. Serogroup B is endemic in Europe and North America, with sporadic outbreaks. However, this serogroup is a major cause of invasive disease and there is currently no effective vaccine. It is our hope that a comparative

For the last few years, Dr. Wilfred Cuff has been working as Mathematical Biologist at CSCHAH, conducting research in the areas of bioinformatics and disease modelling & mapping. His current position draws on past training and experience in zoology, botany, statistics, mathematical modelling and computerized mapping/GIS systems. Dr Cuff is a member of the MITAC's MADI team (Transmission Dynamics and Spatial Spread of Infectious Diseases: Modeling, Prediction and Control) and is currently conducting a spatiotemporal analysis of the Canadian SARS database. His main bioinformatics research interest is in comparative genomics, utilizing the explosion in bacterial sequence data to help focus experimental work onto those sections of the genome with the greatest potential payoff.