jViz.Rna 2.0 is a multi-platform visualization tool
capable of displaying and comparing RNA secondary
structures encoded in a number of file formats. Structures
can be shown using six different visualization modes
including a numerical analysis mode which includes
sensitivity and specificity. Any of the drawings and data
produced can be saved in a variety of formats enabling easy
usage in publications and presentations.
jViz.Rna is built using Java 1.5, enabling usage on Linux, Mac OS X, and Windows.
Flexibility with files
Not only can RNA Structures be loaded from a variety of file types, they can also be converted and saved in any of the supported formats as well. Supported structure file formats are: ConnecT (.ct), Base Pair Sequence (.bpseq), and Dot Bracket Notation (.dbf, .dbn). The resulting visualizations can be saved in the Encapsulated Postscript (.eps) format for high quality vector graphics or the PNG format for other uses.
Load as many structures as you'd like and jViz.Rna will group them by their nucleotide sequence. Show and hide structures by clicking on their checkbox or change their color by clicking on the small color swatch by their filename.
A Choice of Visualizations
Depending on the size and complexity of the structure, you can choose to use the Linear Feynman, Circular Feynman, Dot Plot, Classical Structure, or the Dual Graph visualization mode to display the structure. With the exception of the Dual Graph, which is limited to H-type Pseudoknots, the other visualization modes can display all possible pseudoknot types.
Configurable and Dynamic
Each of the visualization modes has its own set of configurable options. From changing the size of the text to the thickness of the lines, each view can be tweaked to best display your structure. In the Classical Structure mode, the spring model allows you to grab any nucleotide and drag it where you'd like.
Comparison of Structures
All visualization modes are capable of displaying at least two structures with the same sequence overlapped upon each other. Set one of the structures to the native fold of an organism and the other to a prediction to instantly see the accuracy of the prediction. As well, any number of structures can be compared in the Statistics view where the data is summarized in graphs or can be exported to a spreadsheet.