jVIz.Rna - A tool for visual comparison and analysis of RNA secondary structures

RNA is a single stranded biomolecule which can fold back on itself, forming hydrogen bonds. Many projects exist which attempt to predict the 2 dimensional structure that will form from a given nucleotide sequence. Visualization of these predictions helps researchers to better understand the behaviour and results of their prediction algorithms. jViz.Rna is a tool designed to assist in the analysis of structure predictions with three unique features: analysis of multiple structures using seven different visualization methods, dual graphs of RNA structures which highlight the topology of the RNA, and finally, the ability to overlay a predicted structure on top of the native structure of a given RNA in all visualizations apart from dual graphs which use a different comparison method. jViz.Rna is available through http://jviz.cs.sfu.ca. It has been successfully employed on Linux, Mac OS 10.4, and Windows with Java 1.5 or greater.