Date of Award

Spring 2020

Project Type


Program or Major

Computer Science

Degree Name

Master of Science

First Advisor

R D Bergeron

Second Advisor

William K Thomas

Third Advisor

Anthony Westbrook


Comparative genomics focuses on comparing the catalog of genomic elements of whole genome sequences to determine the functional relationship between genes. One of the first steps in comparative analysis is to make genome assemblies for the organisms of interest. However, due to the cost and time required to create these assemblies, only a limited number of organisms can be analyzed simultaneously. A new software package, PALADIN, maps nucleotide reads in protein space using a modified version of the Burrows-Wheeler Aligner (BWA). We demonstrate that PALADIN can accurately and efficiently identify the proteins in a genome using inputs with significantly lower coverage levels than traditional comparative genomics methods. Moreover, we provide an easy to use PALADIN plugin, PB&J, that simplifies the use of PALADIN for comparative genomics.