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Analyses Of Unorthodox Overlapping Gene Segments In Oxytricha Trifallax, Shannon Stich
Analyses Of Unorthodox Overlapping Gene Segments In Oxytricha Trifallax, Shannon Stich
USF Tampa Graduate Theses and Dissertations
A ciliate is a phylum of protozoa that has two types of nuclei, macronuclei and micronuclei. There may be more than one of each type of nucleus in the organism [1]. The macronucleus is the structure where protein synthesis and cell metabolism occur [1]. The micronucleus stores genetic information and is mobilized during a sexual reproduction process called conjugation [1]. The somatic macronucleus (MAC) is developed from the germ-line micronucleus (MIC) through genome rearrangement during a sexual reproduction process called conjugation [6, 8]. Segments of the MIC that form the MAC during conjugation are called macronuclear destined sequences (MDSs) [8]. …
Topological Data Analysis Of Properties Of Four-Regular Rigid Vertex Graphs, Grant Mcneil Conine
Topological Data Analysis Of Properties Of Four-Regular Rigid Vertex Graphs, Grant Mcneil Conine
USF Tampa Graduate Theses and Dissertations
Homologous DNA recombination and rearrangement has been modeled with a class of four-regular rigid vertex graphs called assembly graphs which can also be represented by double occurrence words. Various invariants have been suggested for these graphs, some based on the structure of the graphs, and some biologically motivated.
In this thesis we use a novel method of data analysis based on a technique known as partial-clustering analysis and an algorithm known as Mapper to examine the relationships between these invariants. We introduce some of the basic machinery of topological data analysis, including the construction of simplicial complexes on a data …