What is Comparative Genomics

In this chapter we present PheGeeatHome, a grid-based comparative genomics tool that nominates candidate genes responsible for a given phenotype. A phenotype is the physical manifestation of the interplay of genetic, epigenetic and environmental factors. Our tool is designed to facilitate the discovery and prioritization of candidate genes controlling or contributing to the genetically determined portion of a specified phenotype. However, in order to make reliable nominations of candidate genes from sequence data, several genome-size sequence datasets are required. This makes the approach impractical on traditional computer architectures leading to prohibitively long runtimes. Therefore, we use a computational architecture based on a desktop grid environment and commodity graphics hardware to significantly accelerate PheGee. We validate this approach by showing the deployment and evaluation on a grid testbed for the comparison of microbial genomes.