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Molecular Distance Maps: An Alignment-Free Computational Tool For Analyzing And Visualizing Dna Sequences' Interrelationships, Rallis Karamichalis

Electronic Thesis and Dissertation Repository

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. The …