RNA-DV: an interactive tool for editing and visualizing RNA secondary structures

Although many tools were developed for visualization of RNA secondary structure, RNA-DV is a tool which provides a flexible and powerful interface for RNA secondary structure design and visualization. Being able to dynamically make modification and visualize the result is the most significant contribution of RNA-DV . The ability to allow researcher to make edit and visualize the resulting structure help set apart RNA-DV from other existing tools. The structural modification is achieved through a combination of mouse and keyboard operations. The direct and intuitive interface allows the structure prediction researcher to visualize the structure. Furthermore, RNA-DV provides the necessary tool for structure designers to explore the effect of various structural elements in terms of thermodynamic contributions. Four different thermodynamic energy models ( efn2, HotKnots, Major and RNAeval ) were incorporated allowing users to observe real-time energy changes while designing the structure. Visualizing and editing of pseudo-knotted structure is also supported in RNA-DV .