RNAcanvas: interactive drawing and exploration of nucleic acid structures

Abstract

Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app.

Engineering a Lactobacillus Lysine Riboswitch to Dynamically Control Metabolic Pathways for Lysine Production in Corynebacterium glutamicum

“…plantarum WCFS1 genome, respectively. Subsequently, the secondary structure of the potential lysine riboswitch was predicted by RNAfold [ 31 ] and visualized using RNAcanvas [ 32 ].…”

Characterization of RBM15 protein binding with long noncoding RNAs

“…Chemical probing data for the canonical transcript was mined from the RASP database. Using RNAStructure 52 the secondary structure of each RNA was predicted (using chemical probing data as soft constraints) and the lowest energy structure was visualized using RNAcanvas 53 .…”

RNAscape: geometric mapping and customizable visualization of RNA structure

“…These two-dimensional (2D) diagrams are exclusively driven by base-pairing relationships and laid out in an abstract space. Extensive literature and software ( 5–15 ) describe secondary structure diagrams. However, these representations do not effectively capture tertiary molecular interactions, such as base pairing, stacking, and pseudoknot interactions.…”

“…However, these representations do not effectively capture tertiary molecular interactions, such as base pairing, stacking, and pseudoknot interactions. Therefore, although this approach scales relatively well for large RNA sequences ( 5 ), not considering tertiary interactions can lead to a diagram far from the biological structure and function. More specifically, nucleotides which are positioned relatively close together in three-dimensional (3D) space may appear far away in the visualization.…”