Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization Software

2019

PLoS ONE

Self Cite

Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0’s benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure. Availability : The software is freely available at: https://jviz.cs.sfu.ca/ .

Section: Introductionmentioning

confidence: 99%

jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs

2019

PLoS ONE

Self Cite

“…There are many RNA visualization tools that have been developed, and two excellent reviews of them can be found in [ 9 , 10 ], with notable examples that are still available including VARNA [ 11 ], jViz.RNA [ 12 – 16 ], Forna [ 17 ], PseudoViewer [ 18 – 22 ], 4SALE [ 23 , 24 ], Assemble2 [ 25 , 26 ], RNA2DMap [ 27 ], R2R [ 28 ], and R-Chie [ 29 ]. All Visualization software developed for RNA have as their goal to display an informative structure of the RNA molecule, usually focusing on its secondary structure, that can be annotated and used to convey information in presentations, publications, and any other two-dimensional media.…”

Section: Introductionmentioning

confidence: 99%

Numerical integration methods and layout improvements in the context of dynamic RNA visualization

2017

BMC Bioinformatics

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BackgroundRNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures. One such tool is jViz.RNA. Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation.ResultsComparing the compressed graph and detailed graph implementations, we find that the compressed graph produces results more consistent with RNA drawing conventions. However, we also find that employing the compressed graph method requires a more sophisticated initial layout to produce visualizations that would require minimal user interference. Comparing the two numerical integration methods demonstrates the higher stability of the Backward Euler method, and its resulting ability to handle much larger time steps, a high priority feature for any software which entails user interaction.ConclusionThe work in this manuscript presents the preferred use of compressed graphs to detailed ones, as well as the advantages of employing the Backward Euler method over the Forward Euler method. These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. The results presented demonstrate that both the compressed graph representation, as well as the Backward Euler integrator, greatly enhance the run-time performance and usability. The newest iteration of jViz.RNA is available at https://jviz.cs.sfu.ca/download/download.html.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1682-0) contains supplementary material, which is available to authorized users.

RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots

IEEE/ACM Trans. Comput. Biol. and Bioinf.

2017

RNA visualization is crucial in order to understand the relationship that exists between RNA structure and its function, as well as the development of better RNA structure prediction algorithms. However, in the context of RNA visualization, one key structure remains difficult to visualize: Pseudoknots. Pseudoknots occur in RNA folding when two secondary structural components form base-pairs between them. The three-dimensional nature of these components makes them challenging to visualize in two-dimensional media, such as print media or screens. In this review, we focus on the advancements that have been made in the field of RNA visualization in two-dimensional media in the past two decades. The review aims at presenting all relevant aspects of pseudoknot visualization. We start with an overview of several pseudoknotted structures and their relevance in RNA function. Next, we discuss the theoretical basis for RNA structural topology classification and present RNA classification systems for both pseudoknotted and non-pseudoknotted RNAs. Each description of RNA classification system is followed by a discussion of the software tools and algorithms developed to date to visualize RNA, comparing the different tools' strengths and shortcomings.