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

PLoS One. 2019 May 6;14(5):e0210281. doi: 10.1371/journal.pone.0210281. eCollection 2019.

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. Availability: The software is freely available at: https://jviz.cs.sfu.ca/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology* / methods
  • Computer Graphics
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / genetics*
  • RNA Editing*
  • Software*

Substances

  • RNA

Grants and funding

This work was supported by Natural Sciences and Engineering Council of Canada (http://www.nserc-crsng.gc.ca/index_eng.asp), grant number: 238298-2013-RGPIN (K. W.) and Natural Sciences and Engineering Council of Canada (http://www.nserc-crsng.gc.ca/index_eng.asp), grant number: CGS-D scholarship (B. S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.