Date of Award
Spring 2020
Project Type
Thesis
Program or Major
Computer Science
Degree Name
Master of Science
First Advisor
R D Bergeron
Second Advisor
William K Thomas
Third Advisor
Anthony Westbrook
Abstract
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.
Recommended Citation
Cates, Rachel, "Efficient comparative genomics with low coverage data using PALADIN" (2020). Master's Theses and Capstones. 1338.
https://scholars.unh.edu/thesis/1338