| Over 40 complete poxvirus genomic sequences have been determined over the past decade. For this dissertation research, I have developed and carried out a variety of computational and Statistical studies to reveal the inherent structure of these genomic data to better identify the genetic strategies governing the molecular biology of these viruses, to help delineate some of the genetic features that might play a role in viral pathogenesis, and to more carefully define some of the processes involved in viral evolution. I have predicted the gene content of each genome and regulatory sequences for each gene, analyzed the differences of both the coding regions and regulatory elements of orthologous genes in different strains and species, and used these data to infer the evolutionary history of these viruses at the whole genome level. To accomplish these tasks, I have developed several novel bioinformatics applications and algorithms. These include a generic wrapper application to parallelize and speed up database searching applications onto Linux Cluster, a multiple alignment refiner that uses a genetic algorithm to improve genomic sequence alignments, interpolated context models to predict small functional DNA motifs, and an integrated poxvirus-specific gene prediction and annotation system. |
