CBMS '06 Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems
rnaDesign: local search for RNA secondary structure design
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Although many tools were developed for visualization of RNA secondary structure, RNA-DV is a tool which provides a flexible and powerful interface for RNA secondary structure design and visualization. Being able to dynamically make modification and visualize the result is the most significant contribution of RNA-DV. The ability to allow researcher to make edit and visualize the resulting structure help set apart RNA-DV from other existing tools. The structural modification is achieved through a combination of mouse and keyboard operations. The direct and intuitive interface allows the structure prediction researcher to visualize the structure. Furthermore, RNA-DV provides the necessary tool for structure designers to explore the effect of various structural elements in terms of thermodynamic contributions. Four different thermodynamic energy models (efn2, HotKnots, Major and RNAeval) were incorporated allowing users to observe real-time energy changes while designing the structure. Visualizing and editing of pseudo-knotted structure is also supported in RNA-DV.