TBI-Preprint 06-07-001
Download:
Titel:
Visualization of Barrier Tree Sequences
Author(s):
Christian Heine,
Gerik Scheuermann,
Christoph Flamm,
Ivo L. Hofacker,
Peter F. Stadler
Submitted to:
InfoVis 2006
Abstract:
Dynamical models that explain the formation of spatial structures of
RNA molecules have reached a complexity that requires novel
visualization methods that help to analyze the validity of these
models. Here, we focus on the visualization of so-called folding
landscapes of a growing RNA molecule. Folding landscapes describe the
energy of a molecule as a function of its spatial configuration; thus
they are huge and high dimensional. Their most salient feature,
however, are encapsulated by their so-called barrier tree that
reflects the local minima and their connecting saddle points. For each
length of the growing RNA chain there exists an folging landscape. We
visualize the sequence of folding landscapes by an animation of the
corresponding barrier trees. To do that, we adapt the foresight layout
with tolerance algorithm for general dynamic graph layout
problems. Since it is very general, we give detailed account to each
phase: constructing a supergraph for the trees, layout of that
supergraph using a modified dot algorithm, and presentation techniques
for the final animation.
Keywords:
Graph drawing,
dynamic graph,
RNA folding,
energy landscape,
fitness landscape,
barrier tree
Return to 2006 working papers list.
Last modified: 2006-08-09 16:31:54 xtof