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RNAStructViz can be installed from-source on Mac/Linux/Unix systems of all varieties provided you provided you have a few prerequisites (primarily cairo and a modern version of FLTK). The most recent officially "stable" source release of our software is archived here. Mac users also have the convenient option of installing our custom made Brew packages, which includes a gtDMMB-sponsored tap of the current (now working) 1.4.x FLTK GUI library which many Mojave users will require to get the otherwise hard-to-install library functionally up and running on their systems. The following provides a quick list of our available install procedures on common supported platforms:
- Mac OSX Homebrew installer instructions are found here
- Linux / (BSD)Unix platform instructions for from-source installs are found here
- Specific Mac OSX from-source installation instructions are found here
- Caveats for the unsupported Windows 10 platform users are explained here
This is the metaphorical "horse's mouth" with respect to user documentation for the features in the RNAStructViz RNA structure viewer and graphical comparison tool. We are affiliated with and supported by the gtDMMB (Georgia Tech research group in Discrete Math and Molecular Biology) led by Prof. Christine Heitsch. You can see the details of our funding sources here. The application is primarily a graphical comparison tool for RNA secondary structures, but also includes a color-coded CT file viewer and graphically-based comparative statistics.
More precisely, RNAStructViz is an open source GUI for viewing and visualizing RNA structures encoded in the CT and FASTA file formats (see also here and here for more information on the CT file format). Examples of such files can be found in online databases including the NCBI databases, here (example.ct), here (RA7680.ct), and in the following databases (FASTA formatted): RefSeq, BLAST, TraceDB, UniGene, and UniVec. There are also external programs for conversions between the DOT bracket and CT file formats: ct2dot (online interface) and dot2ct (online interface).
We provide the following links to documentation on the core features and functionality of this application:
- RNA secondary structure visualization. Generate arc diagrams comparing up to three secondary structures using color and transparency. Also includes an export tool allowing generated images to be saved to disk for later use. Screenshot.
- Statistics comparing multiple predicted structures. Given a reference structure, compare multiple predictions on the same sequence by calculating statistics including number of true positives, false positives, false negatives, sensitivity, selectivity, and positive values. Also generates ROC plots and allows exporting of computed statistics in plain text format. Screenshot 1 and screenshot 2.
- CT file viewer. View CT files, with color coding, without leaving RNAStructViz.
- Customization options and UI themes.Fine tune many aspects of the RNAStructViz user interface. Users withaccessibility needs (in particular, those with color contrast needs) can tweak most of the colors used in the application, including using especially contrasting (or non-contrasting) color choices in the UI.
Bug reports, feature requests, and general support inquiries may be posted in the GitHub issues threads which we track for the project. The developers and our gtDMMB group as a whole will try to keep up with the requests users submit and archive here. Any requests for missing, or confusing documentation, associated with our current WIKI site should also be posted as a new issue in this forum or reported by contacting one of the core developers listed in the footer information on this page.