Title of Thesis: a Web-based Interactive Visualization Tool to Explore Patterns of Amino Acid Substitution a Web-based Interactive Visualization Tool to Explore Patterns of Amino Acid Substitution

Title of Thesis: A web-based interactive visualization tool to explore patterns of amino acid substitution Kamalika Das, Master of Science, 2005 Thesis directed by: Dr. Penny Rheingans Among all the natural sciences, biology is the most data-rich subject. A few central databases of biology are growing exponentially in size with time. There has also been an exponential increase in the diversity of specialized databases in the last decade. These vast repositories of data contain valuable information relevant to cutting-edge biological research, such as research on genetic evolution. In their attempts to explain evolution, biologists, to date, have relied on observations alone to explain the divergence of protein sequences to form different types of organisms. Since amino acids are the basic building blocks of protein molecules, understanding the effect of the properties of amino acids in the substitution process might give biologists insight into genetic evolution. In this research, we represent the relationship among the different amino acids and their physiochemical properties using a graph-based visualization technique. We have developed a number of new visualization schemes for aiding the understanding of the relationship between amino acids’ properties and amino acid substitution patterns so that biologists can explain the observations in genetic evolution in the form of a scientific cause-and-effect model. A web-based interactive visualization tool to explore patterns of amino acid substitution