Table 1.
Comparison of programs for 2D drawing of nucleic acid structures. Solid dots indicate that a feature is supported by a program, though the robustness of feature implementations may vary between different programs. VARNA and jViz.RNA have hollow dots for web-based use since they require a Java plugin for use in a web browser. Point-and-click structure editing refers to the ability to add and remove base-pairs and interactions in the secondary and tertiary structures of a drawing graphically using the mouse. Motif finding functionality refers to features similar to the Find Motifs form in RNAcanvas. Point-and-click element editing is the ability to select individual or groups of elements to edit by clicking on them and/or dragging a selecting box over them, rather than being required to select elements by less direct means (e.g. by inputting numeric positions). Text labels for structural features refer to the ability to place pieces of text next to structural features such as hairpins and linker regions that name them. Flexible base numbering is the ability to assign any number to any base regardless of what numbers are assigned to other bases. This is useful when a drawing contains two discontinuous portions of a larger sequence and the numbering for one portion must be offset from the other. Granular output scaling refers to the ability to scale drawings at the level of individual elements when exported, as opposed to scaling an exported drawing as a whole after export. Drawing using input files and automated drawing are grouped together since the use of input files can lend itself to automated drawing via the automated creation of input files. Automated drawing also includes the ability to generate large numbers of structure drawings in an automated way in general, such as by allowing other software written by the user to interface with the structure drawing software, such as with VARNA
| RNAcanvas | VARNA | XRNA | PseudoViewer | RnaViz | jViz.RNA | forna | RiboSketch | RNAView | R2R | R2DT | RNArtist | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Web-Based | • | ○ | • | • | ○ | • | • | • | • | |||
| Click-and-Drag Layout Adjustment | • | • | • | • | • | • | • | |||||
| Force-Based Drawing Layouts | • | • | • | |||||||||
| Draggable, Curved Tertiary Bonds | • | |||||||||||
| Incorporation of Pseudoknots into the Layout | • | • | • | • | • | • | • | • | ||||
| Point-and-Click Structure Editing | • | • | • | • | • | • | • | |||||
| Real-Time Highlighting of Complementary Sequences | • | |||||||||||
| Motif Finding Functionality | • | |||||||||||
| Point-and-Click Element Editing | • | • | • | • | • | • | ||||||
| Leontis-Westhof Notation | • | • | • | • | • | • | ||||||
| Text Labels for Structural Features | • | • | • | |||||||||
| Flexible Base Numbering | • | |||||||||||
| SVG Output | • | • | • | • | • | • | • | • | • | |||
| PPTX Output | • | |||||||||||
| Granular Output Scaling | • | |||||||||||
| Raster Image Output (e.g. PNG, TIFF, JPEG) | • | • | • | • | • | • | • | • | • | • | ||
| Template-Based Drawing | • | • | ||||||||||
| Drawing Using Input Files and Automated Drawing | • | • | • | • | • | • |