jViz.RNA 4.0 - Advanced integration methods, pseudoknot visualization, and online editing in the context of RNA secondary structure visualization

RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures; one such tool is jViz.RNA 2.0. Currently, jViz.RNA 2.0 employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA 2.0 in four areas: First, the drawing of RNA secondary structures according to common drawing conventions employing a new underlying graph representation. Second, employing advanced numerical integration methods (the Backward Euler Method) to achieve dramatic run-time performance improvements utilizing the new graph implementation. Third, the ability to classify and visualize pseudoknots was added to jViz.RNA in order to extend the set of RNA structures that can be visualized. Finally, online base-pair removal and addition capabilities were incorporated into jViz.RNA in the interest of providing users with the capacity to modify, edit, and create RNA molecules from existing alternative representations (e.g. images or drawings). With regards to results, comparing the compressed graph and detailed graph implementations, it was found that the compressed graph produces results more consistent with RNA drawing conventions, and does so noticeably faster. Additionally, the advantages of the Backward Euler method as a more stable approach to mitigate interactions between users and the RNA model, allowing users to better and faster manipulate the RNA model, have been shown conclusively. The incorporation of pseudoknot visualization capacities demonstrated a new high degree of utility and flexibility since users are now able to visualize the majority, if not entirety, of biologically known RNAs, as well as modify the given pseudoknot representation. The implementation of online structure editing functionality allows users to construct related or theoretical molecules from existing ones, as well as construct arbitrary RNA structures from their primary nucleotide sequence