Date of Award

Fall 2022

Document Type

Open Access Dissertation


College of Pharmacy

First Advisor

Michael Shtutman


Sequencing technology has advanced greatly over the past couple of decades. This has led to many studies developing hypotheses based on genomic data. This requires many genomic studies to have up-to-date information on the species’ or subject’s genome being investigated. If a study does not have accurate or up-to-date background information, then they cannot fully develop their theories that are being established. In this study, I utilize outbred Peromyscus maniculatus, deer mice that are genetically diverse, to record the polymorphisms that are found throughout the Peromyscus maniculatus genome. I first explore the differences between the polymorphisms found in Peromyscus maniculatus bairdii and Peromyscus maniculatussonoriensis , two subspecies of Peromyscus maniculatus. I then create an artificial genome for sonoriensis for the purposes of investigating if a new reference genome can be developed and effectively utilized by using a known homogenous reference genome and polymorphisms and if there are large differences between the sonoriensis and bairdii genomes. This was simultaneously done while looking at GPU and CPU-based computation of whole genome sequencing analysis and the time it takes between the GPU and CPU methods for WGS analysis. I finally investigated the polymorphisms found in Peromyscus maniculatus to determine which single nucleotide polymorphisms that correlate with the variable levels of the unfolded protein response that is seen in Peromyscus maniculatus.


© 2022, Matthew Dixon Lucius