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Full-Text Articles in Physical Sciences and Mathematics
Patterns In Words Related To Dna Rearrangements, Lukas Nabergall
Patterns In Words Related To Dna Rearrangements, Lukas Nabergall
USF Tampa Graduate Theses and Dissertations
Patterns, sequences of variables, have traditionally only been studied when morphic images of them appear as factors in words. In this thesis, we initiate a study of patterns in words that appear as subwords of words. We say that a pattern appears in a word if each pattern variable can be morphically mapped to a factor in the word. To gain insight into the complexity of, and similarities between, words, we define pattern indices and distances between two words relative a given set of patterns. The distance is defined as the minimum number of pattern insertions and/or removals that transform …
Properties Of Graphs Used To Model Dna Recombination, Ryan Arredondo
Properties Of Graphs Used To Model Dna Recombination, Ryan Arredondo
USF Tampa Graduate Theses and Dissertations
A model for DNA recombination uses 4-valent rigid vertex graphs,
called assembly graphs. An assembly graph,
similarly to the projection of knots, can be associated with an
unsigned Gauss code, or double occurrence word.
We define biologically motivated reductions that act on double
occurrence words and, in turn, on their associated assembly graphs. For
every double occurrence word w there is a sequence of reduction
operations that may be applied to w so that what remains is the
empty word, [epsilon]. Then the nesting index of a word w,
denoted by NI(w), is defined to to be …