Abstract
DNA is a complex molecule that consists of biological information that is passed down from generation to generation. With the evolution over time, there are different kinds of species that evolved from a common ancestor because of the occurrence of DNA sequence rearrangements. DNA sequence similarity analysis is a major challenge since the number of sequences is rapidly increasing in the DNA database. In this research, we based a mathematical method to analyze the similarity of two DNA sequences using Graph Theory. This mathematical method started by modeling a weighted directed graph for each DNA sequence, constructing its adjacency matrix, and converting it to the representative vector for each graph. From these vectors, the similarity was determined by distance measurements such as Euclidean, Cosine, and Correlation. By keeping this method as the based method, we will check whether it is applicable for any DNA fragments in considered genomes and molecular similarity coefficients can be used as distance measurements. We will obtain similarities using the graph spectrum instead of the representative vector. Then we will compare the results from the representative vector and that of the graph spectrum. The modified method is tested by using the mitochondrial DNA of Human, Gorilla, and Orangutan. It gives the same result when the number of nucleotides in DNA fragments is increased.
Highlights
Deoxyribonucleic acid or DNA is a complex molecule that consists of the biological information that makes every species distinctive
Research Methodology The materials used in this research are mitochondrial DNA sequences of three evolutionary closed species (Human, Orangutan, and Gorilla) that were downloaded from Gen Bank of National Center for Biotechnology Information (NCBI)
We applied the novel method to determine the evolutionary closeness between Human, Gorilla, and Orangutan
Summary
Deoxyribonucleic acid or DNA is a complex molecule that consists of the biological information that makes every species distinctive. It includes the instructions an organism needs to develop, live, and reproduce. Deoxyribonucleic acid is created of chemical building blocks known as nucleotides. Each building block contains a phosphate group, a sugar group, and a nitrogen base. Nucleotides are arranged in two long strands that form a spiral called a double helix. Nitrogen bases are available in four types. They are adenine (A), thymine (T), guanine (G), and cytosine(C). The biological instructions or genetic code contained in a DNA strand is determined by the order or sequence of these bases
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