Four-regular graphs with rigid vertices associated to DNA recombination

Genome rearrangement and homological recombination processes have been modeled by Angeleska et al. [A. Angeleska, N. Jonoska, M. Saito, DNA recombinations through assembly graphs, Discrete Appl. Math. 157 (2009) 3020–3037] as 4-regular spacial graphs with rigid vertices, called assembly graphs. These graphs can also be represented by double occurrence words called assembly words. The rearranged DNA segments are modeled by certain types of paths in the assembly graphs called polygonal paths. The minimum number of polygonal paths visiting all vertices in a graph is called an assembly number for the graph.In this paper, we give formulas for counting certain types of assembly graphs and assembly words. Some of these formulas produce sequences not previously reported at the Online Encyclopedia of Integer Sequences (http://oeis.org). We provide a sharp upper bound for the number of polygonal paths in Hamiltonian sets of polygonal paths, and present a family of graphs that achieves this bound. We investigate changes in the assembly numbers as a result of graph compositions. Finally, we introduce a polynomial invariant for assembly graphs and show properties of this invariant.