RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences

ABSTRACT RNA structure prediction programs remain imperfect and many substructures are still identified by manual exploration, which is most efficiently conducted within an RNA structure drawing program. However, most nucleic acid structure drawing programs have limited capability for structure modification (i.e., breaking and forming new bonds between bases), often requiring that the structure notation be textually edited. RNA2Drawer was developed to allow for graphical structure editing while maintaining the geometry of a drawing (e.g., ellipsoid loops, stems with evenly stacked base pairs) throughout structural changes and manual adjustments to the layout by the user. In addition, the program allows for annotations such as colouring and circling of bases and drawing of tertiary interactions (e.g., pseudoknots). RNA2Drawer can also draw commonly desired elements such as an optionally flattened outermost loop and assists structure editing by automatically highlighting complementary subsequences, which facilitates the discovery of potentially new and alternative pairings, particularly tertiary pairings over long-distances, which are biologically critical in the genomes of many RNA viruses and cannot be accurately predicted by current structure prediction programs. Additionally, RNA2Drawer outputs drawings either as PNG files, or as PPTX and SVG files, such that every object of a drawing (e.g., bases, bonds) is an individual PPTX or SVG object, allowing for further manipulation in Microsoft PowerPoint or a vector graphics editor such as Adobe Illustrator. PowerPoint is the standard for presentations and is often used to create figures for publications, and RNA2Drawer is the first program to export drawings as PPTX files.

[1]  Robert E. Bruccoleri,et al.  An improved algorithm for nucleic acid secondary structure display , 1988, Comput. Appl. Biosci..

[2]  Zasha Weinberg,et al.  R2R - software to speed the depiction of aesthetic consensus RNA secondary structures , 2011, BMC Bioinformatics.

[3]  David Hoksza,et al.  TRAVeLer: a tool for template-based RNA secondary structure visualization , 2017, BMC Bioinformatics.

[4]  K. Weeks,et al.  Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution , 2006, Nature Protocols.

[5]  E. Westhof,et al.  Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.

[6]  Rupert De Wachter,et al.  RnaViz 2: an improved representation of RNA secondary structure , 2003, Bioinform..

[7]  Eric Westhof,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[8]  Eckart Bindewald,et al.  RiboSketch: versatile visualization of multi‐stranded RNA and DNA secondary structure , 2018, Bioinform..

[9]  Yanga Byun,et al.  PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures , 2006, Nucleic Acids Res..

[10]  A. Simon 3'UTRs of carmoviruses. , 2015, Virus research.

[11]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[12]  Beth L. Nicholson,et al.  Functional long-range RNA–RNA interactions in positive-strand RNA viruses , 2014, Nature Reviews Microbiology.

[13]  B A Shapiro,et al.  STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis. , 1996, Journal of molecular graphics.

[14]  Boris Shabash,et al.  jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs , 2019, PloS one.

[15]  Ivo L. Hofacker,et al.  Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams , 2015, Bioinform..

[16]  Bruce A. Shapiro,et al.  Generating non-overlapping displays of nucleic acid secondary structure , 1984, Nucleic Acids Res..

[17]  Yann Ponty,et al.  VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..

[18]  Eric Westhof,et al.  Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure , 2005, Bioinform..