RnallViewer is an RNA analysis and visualization tool that combines information and processing from various command-line tools in an intuitive graphical user interface (GUI). Rnall is used for generating RNA structure predictions, which can be automatically sent to Naview, plt22ps, and Ghostscript for visualization. Annotation information can be included, parsed with the help of BioJava. RnallViewer's panelling system allows much of this information to be displayed simultaneously, and comprehensive searching methods allow quick access to specific regions based on annotation and position criteria in the format of NCBI ptt format (see an example).

License

RnallViewer was jointly developed by Peter P. Dempsey, Xiu-Feng (Henry) Wan, and Dong Xu. It is freely available under the GNU license for academic users. The latest version is HERE.

System Requirements

RnallViewer works on Java-compatible machines and has been tested on Windows and OS X. RnallViewer requires Java 1.5 or higher(download site) and Java3D (download site). RnallViewer's installer includes some other third-party programs and technologies which can be installed independently if desired, such as Ghostscript, BioJava, Naview and plt22ps. If you are not working under Windows you must install Ghostscript yourself as there is currently not automated installer for other OSes.

Contact

We welcome contributions to RnallViewer, particularly suggestions and bug reports. If you have bug reports, questions, comments or suggestions, please contact Xiu-Feng (Henry) Wan by e-mail: wan@cvm.msstate.edu.

Acknowledgement

This work has been supported by the US Department of Energy's Genomes to Life program (http://www.doegenomestolife.org) under project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling" (http://www.genomes-to-life.org).

If you wish to acknowledge the use of Rnall Viewer in a publication, you should cite:

  • Wan, X.-F., G. Lin, and D. Xu. 2006. Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes. Journal of Bioinformatics and Computational Biology, 4: 1015-1031.
  • Wan, X.-F., P. P. Dempsey, and D. Xu. 2008. RnallViewer: A tool for RNA local secondary structure prediction, localization, and visualization. International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, 2(5): 607-612.