Physical Sciences and Mathematics Commons^™

Discrete Models And Algorithms For Analyzing Dna Rearrangements, Jasper Braun

USF Tampa Graduate Theses and Dissertations

In this work, language and tools are introduced, which model many-to-many mappings that comprise DNA rearrangements in nature. Existing theoretical models and data processing methods depend on the premise that DNA segments in the rearrangement precursor are in a clear one-to-one correspondence with their destinations in the recombined product. However, ambiguities in the rearrangement maps obtained from the ciliate species Oxytricha trifallax violate this assumption demonstrating a necessity for the adaptation of theory and practice.

In order to take into account the ambiguities in the rearrangement maps, generalizations of existing recombination models are proposed. Edges in an ordered graph model …