1 Structural bioinformatics PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

Motivation: Pseudoknots in RNA structures make visualization of RNA structures difficult. Even if a pseudoknot itself is represented without a crossing, visualization of the entire RNA structure with a pseudoknot often results in a drawing with crossings between the pseudoknot and other structural elements, and requires additional intervention by the user to ensure that the structure graph is overlap-free. Many programs such as web services prefer to obtain an over-lap-free graph in one-shot rather than get a graph with overlaps to be edited. There are few programs for visualizing RNA pseudoknots, and PseudoViewer has been the almost only program that automati-cally draws RNA secondary structures with pseudoknots. The previ-ous version of PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some hypothetical pseudoknots as nonplanar drawings. Results: We developed a new version of PseudoViewer for effi-ciently visualizing large RNA structures with any types of pseudok-nots, both known and hypothetical, as planar drawings in one-shot. It is about 10 times faster than the previous algorithm, and produces a more compact and aesthetic structure drawing. PseudoViewer3 supports both web services and web applications. Availability: The new version of PseudoViewer, PseudoViewer3, is available a