Degree Year
2016
Document Type
Thesis - Open Access
Degree Name
Bachelor of Arts
Department
Mathematics
Advisor(s)
Robert Bosch
Keywords
Quadratic assignment problem, QAP, Discrete optimization, Simulated annealing, Hill climbing, DNA sequence representation
Abstract
We explore methods for drawing a graph of DNA sequences on a digital canvas such that the Euclidean distances between sequences on the canvas suggest the distances between the sequences as calculated from pairwise sequence alignment. We use data from three plant taxa, the genus Castilleja as well as the families Caryophyllaceae and Cactaceae, to test our methods. We discuss different possible measures of the cost of a drawing, and analyze heuristic approaches to the problem including random assignment, greedy assignment, the iterated hill-climber, and simulated annealing. We find that our hill-climbing method tends to return superior drawings. Our simulated annealing method also returns drawings with low costs, but in much less time than the hill-climbing method for large datasets.
Repository Citation
Olivieri, Julia, "Drawing DNA Sequence Networks" (2016). Honors Papers. 239.
https://digitalcommons.oberlin.edu/honors/239
