Visualization of Barrier Tree Sequences Revisited

Abstract

Summary. The increasing complexity of models for prediction of the native spatial structure of RNA molecules requires visualization methods that help to analyze and understand the models and their predictions. This paper improves the visualization method for sequences of barrier trees previously published by the authors. The barrier trees of these sequences are rough topological simplifications of changing folding landscapes -energy landscapes in which kinetic folding takes place. The folding landscapes themselves are generated for RNA molecules where the number of nucleotides increases. Successive landscapes are thus correlated and so are the corresponding barrier trees. The landscape sequence is visualized by an animation of a barrier tree that changes with time.The animation is created by an adaption of the foresight layout with tolerance algorithm for dynamic graph layout problems. Since it is very general, the main ideas for the adaption are presented: construction and layout of a supergraph, and how to build the final animation from its layout. Our previous suggestions for heuristics lead to visually unpleasing results for some datasets and, generally, suffered from a poor usage of available screen space. We will present some new heuristics that improve the readability of the final animation.

DrForna: visualization of cotranscriptional folding

“…This could in principle be used to view the most occupied structure from an ensemble, but then large structural transitions would appear sudden and unexpected. Alternatively, Heine et al (2008) show movies of dynamically changing energy landscapes during transcription. This approach is specifically designed to visualize output of the coarse-grained cotranscriptional folding software BarMap ( Hofacker et al 2010 ), and it does not visualize the respective secondary structures.…”