Date of Thesis
Sequence comparison, or the process of determining the similarity between two sequences, is an important topic in mathematics, statistics, and computer science, and has applications to an even wider number of fields, including in biology and medicine. Traditionally, sequence comparison is applied to the discovery of similar genomes, however other sequence data involves events in time. The inclusion of the measures of time between subsequent events is absent from most sequence comparison calculations. Extending the Smith-Waterman and Needleman-Wunsch algorithms, which are two quintessential algorithms used for sequence comparison, a method is proposed to take advantage of these measures of time between elements organized in a finite sequence. This will allow for a better measure of similarity between two sequences in time. Using a simulation study, these algorithms are shown to be able to distinguish between sequences with different variations in their time gaps effectively. A new time parameter is introduced to allow for tuning the importance of time in the calculation as compared to the importance of the sequence variation. These algorithms are then applied to eye-tracking data of autism patients, and the inclusion of time is shown to improve the algorithms' abilities to distinguish between autistic and non-autistic patients. Ultimately, the approach is concluded to effectively include variations in time in the calculation of the Smith-Waterman and Needleman-Wunsch algorithms.
Dynamic Programming, Dynamic Time Warping, Sequence Comparison, Algorithms, Clustering, Classification
Honors Thesis (Bucknell Access Only)
Bachelor of Science
Minor, Emphasis, or Concentration
Women's and Gender Studies
Murph, Alexander C., "Comparing Finite Sequences of Discrete States with Non-uniform Time Intervals" (2018). Honors Theses. 434.