TangleSolve : a topological tool used in the analysis of site-specific recombination

Site-specific recombinases are naturally occurring enzymes that catalyze the\ud exchange of genetic material between specific sites on DNA. The Tangle\ud Method is a mathematical tool that models the topological mechanism of binding\ud and strand-exchange in a recombination reaction. The Tangle Method\ud addresses strand-exchange using two tangle equations that are solvable when\ud the tangles are rational or sums of rational tangles. These equations are solved\ud by the java applet TangleSolve. This thesis provides an expository presentation\ud of the Tangle Method and its applications to Xer recombinase and Tn3 resolvase.\ud We have made TangleSolve more accessible to a wider scientific community by\ud improving its website and creating an online tutorial. We have also extended\ud TangleSolve further addressing single and multiple recombination using the Buck\ud and Flapan Method. We provide a comparison of both methods through\ud computer implementation using our recombination examples