Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation

Abstract

I performed computational analyses of various approaches to generating re- engineered versions of the genome of bacteriophage T7. I analyzed a proposed design for a re-engineered genome by examining conservation of T7 genes across related phages, and looking for RNA secondary structure arising from the re-engineered genome that might contribute to unwanted regulation. In addition, I proposed two methods of generating libraries of T7 genomes, and implemented simulations showing that the proposed methods are theoretically feasible. I conclude with thoughts on how to further validate my proposed approaches to genome generation, and suggest a specific high-throughput method of characterizing rebuilt genomes.