jViz.RNA 4.0—Visualizing Pseudoknots and RNA Editing Employing Compressed Tree Graphs

Resource type
Date created
2019-05-06
Authors/Contributors
Abstract
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.
Document
Published as
Shabash B, Wiese KC (2019) jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs. PLoS ONE 14(5): e0210281. DOI: 10.1371/journal.pone.0210281.
Publication title
PLoS ONE
Document title
jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs
Date
2019
Volume
14
Issue
5
Publisher DOI
10.1371/journal.pone.0210281
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
Member of collection
Attachment Size
journal.pone_.0210281.pdf 5.06 MB