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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 …