SoftwareComparisions

Comparison of graphical software for RNA secondary structure analysis

List of related software

We compare related graphically oriented software for RNA secondary structure comparison including the following applications:

1. R-chie: Produces various forms of arc diagrams for secondary structures
2. VARNA: Java-applet-based viewer of radial layout diagrams for secondary structures
3. RNAbows: Web interface combining multiple RNA software packages
4. Forna: RNA secondary structure visualization using a force directed graph layout
5. jViz.rna: Supports a GUI based view of radial diagrams for structures and pseudo knot visualization

Feature-by-feature comparison chart notation

The following tables compare the features of other software applications with visualization features similar to that of RNAStructViz. In the table, the columns denote inclusion of the features listed to the left as rows. We use ✔️ to denote that a particular application implements a key feature specification, ❌ to denote that an application does not implement a key listed feature, and 〰️ to denote a partial implementation. We also use 💥 or 〰️ to denote partial OS platform support, e.g., Windows support should work, but is not confirmed by our tests. Where possible, we attempt to annotate the wide bins we use to classify the features of these applications with footnotes given below the table. This table was last compiled in August of 2020 with the current feature set implemented by each program.

Tables of features supported by each application

Platform and availability

Feature \ Application	RNAStructViz	R-chie	VARNA	RNAbows	Forna	jViz.rna
Mac OSX support	✔️	✔️	✔️	✔️	✔️	✔️
Linux / Unix support	✔️	✔️	✔️	✔️	✔️	✔️
Windows support	💥	✔️	✔️	✔️	✔️	✔️
Open source software?	✔️	✔️	✔️	❌	✔️	〰️ [1]
License	GPL-V3	GPL-V3	GPL	None	Apache	GPL
Core programming language?	C++	R	Java	❓	Python, JavaScript	Java (binary distribution)
Requires external libraries?	✔️	〰️ (within R)	✔️	❌	〰️ [2]	✔️

Notes:

[1]: If you use jViz.Rna or images created from jViz.Rna in your work or publications, you must cite their article as credit for the original derivative work they have done with open source software (vanilla GPL). The source is not freely available on the downloads site.

[2]: External and portable javascript libraries that are easy and seamless to import

Software usability criteria

Feature \ Application	RNAStructViz	R-chie	VARNA	RNAbows	Forna	jViz.rna
Graphical user interface (GUI)	✔️	〰️	✔️	✔️	✔️	✔️
Command line interface (CLI)	〰️ [1]	✔️ (standard R language CLI)	❌	❌	❌	❌
Web interface	❌	✔️	❌	✔️	✔️	❌
Multi-window interface	✔️	❌	〰️	❌	❌	〰️
Can compare two structures at once	✔️	✔️	❌	✔️	✔️ [2]	❌
Can compare three structures at once	✔️	❌	❌	❌	✔️ [2]	❌
Can compare 4+ structures at once	❌	❌	❌	❌	✔️ [2]	❌
Allows specialized colorings of structures?	✔️	✔️	✔️	❌	✔️	✔️

Notes:

[1]: Supports extended options and settings that can be configured on the command line at runtime

[2]: We make a point to contrast with the support for structural comparisons in RNAStructViz. The FORNA library (and online demo site) allows an arbitrary number of structures to visualized on-screen at a single time. At the time of this comparison, the software does not enable users to make live comparisons between common base pairs for structures with the same base sequences. Consult the developer documentation for its capabilities for reference.

Support of standard text formats for secondary structures

Feature \ Application	RNAStructViz	R-chie	VARNA	RNAbows	Forna	jViz.rna
Supports CT files	✔️	✔️	✔️	❌	❌	✔️
Supports DOT (Dot Bracket) files	✔️	✔️	✔️	❌	〰️ [3]	✔️ [1]
Structure text file viewer bundled?	✔️	❌	✔️ [2]	❌	❌	❌
Requires specialized format to run?	❌	❌	❌	❌	〰️	❌
Ability to convert to other structure formats (non-image)?	✔️	❌	❌	❌	❌	✔️
Ability to edit sequence data?	❌	❌	✔️	✔️	✔️	✔️

Notes:

[1]: Requires a specialized .dbf file extension in the format in place of more standard .dot or .dbn

[2]: Has an integrated editor for the base sequences and pairing data that users can use as a viewer

[3]: Uses a hybrid of this notation passed by separate strings at runtime

Graphical views available in the software and diagram type support

Feature \ Application	RNAStructViz	R-chie	VARNA	RNAbows	Forna	jViz.rna
Ability to generate comparitive stats	✔️	✔️ [4]	❌	✔️	❌	❌
Plots circular arc diagrams	✔️	✔️➕	❌	✔️	❌	〰️ [1]
Plots labeled radial diagrams	✔️	❌	✔️➕	❌	✔️	✔️
Plots linear diagrams	❌	✔️	❌	〰️ [3]	❌	❌
Other diagram types supported	✔️ [2]	✔️	❌	✔️	❌	❌

Notes:

[1]: To a certain extent with pseudo knotted structures

[2]: ROC plots can be viewed in the statistics window

[3]: Plots four distinct types of hybrid arc diagrams along an axis

[4]: Incorporated as part of the plot legends