Western University Scholarship@Western Electronic Thesis and Dissertation Repository September 2016 Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences' interrelationships Rallis Karamichalis The University of Western Ontario Supervisor Prof. Lila Kari The University of Western Ontario Graduate Program in Computer Science A thesis submitted in partial fulfillment of the requirements for the degree in Doctor of Philosophy © Rallis Karamichalis 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Other Computer Sciences Commons Recommended Citation Karamichalis, Rallis, "Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences' interrelationships" (2016). Electronic Thesis and Dissertation Repository. 4071. https://ir.lib.uwo.ca/etd/4071 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact
[email protected]. Abstract In an attempt to identify and classify species based on genetic evidence, we propose a novel combination of methods to quantify and visualize the interrelationships between thousand of species. This is possible by using Chaos Game Representation (CGR) of DNA sequences to compute genomic signatures which we then compare by computing pairwise distances. In the last step, the original DNA sequences are embedded in a high dimensional space using Multi- Dimensional Scaling (MDS) before everything is projected on a Euclidean 3D space. To start with, we apply this method to a mitochondrial DNA dataset from NCBI containing over 3,000 species.