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IEEE Transactions on Visualization and Computer Graphics
Article . 2006 . Peer-reviewed
License: IEEE Copyright
Data sources: Crossref
DBLP
Article . 2020
Data sources: DBLP
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Visualization of Barrier Tree Sequences

Authors: Christian Heine 0002; Gerik Scheuermann; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler;

Visualization of Barrier Tree Sequences

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 features, 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 a folding landscape. We visualize the sequence of folding landscapes by an animation of the corresponding barrier trees. To generate the animation, we adapt the foresight layout with tolerance algorithm for general dynamic graph layout problems. Since it is very general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a modified DoT algorithm, and presentation techniques for the final animation.

Countries
Germany, Austria
Related Organizations
Keywords

ddc:004, 1040 Chemie, Models, Molecular, Base Sequence, Sequence Analysis, RNA, Molecular Sequence Data, User-Computer Interface, Models, Chemical, Computer Graphics, Nucleic Acid Conformation, RNA, Computer Simulation, 1040 Chemistry, Visualization, RNA, Computer science, Animation, info:eu-repo/classification/ddc/004

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    popularity
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    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
13
Average
Top 10%
Average
Green
bronze