Nucleic Acid Software

• FR3D, a software for finding local and composite recurrent structural motifs in RNA 3D structures.
  • Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol, 56, 215-252.
• RNAView, a program for quickly generating a display of RNA/DNA secondary structures with tertiary interactions.
  • Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res, 31, 3450-3460.
• 3DNA, a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
  • Lu, X.J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res, 31, 5108-5121.
• The UNAFold Web Server is an amalgamation of two existing web servers: mfold & DINAMelt.
  • Markham, N. R. & Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581.
  • Markham, N. R. & Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Function and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3–31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.
• Sfold, software for statistical folding of nucleic acids and studies of regulatory RNAs.
  • http://sfold.wadsworth.org.
  • Ding, Y., Chan, C.Y. and Lawrence, C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166.
  • Ding, Y. and Lawrence, C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 31, 7280-7301.
• RNAMotifScan, a tool for automatic comparing and searching for RNA tertiary motifs using secondary structural alignment.
  • Zhong, C., Tang, H. , and Zhang, S. (2010) "RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment", Nucleic Acids Research.
• VARNA, a visualization applet for RNA.
  • Darty, K., Denise, A., Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
• SARA-Coffee, accurate multiple RNA structural alignment.
  • Kemena, C., Bussotti, G., Capriotti, E., Marti-Renom, MA, Notredame, C. (2013) Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinformatics. 29(9),1112-9.
• Assemble2, allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.
  • Jossinet, F., Ludwig, T. E. & Westhof, E. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26, 2057–9.
• MINT, an automatic tool for analysing three-dimensional structures of RNA and DNA molecules, their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or NMR-derived structures).
• DSSR, an integrated software tool for investigating the three-dimensional architecture of RNA structures.
• CoSSMos, Characterization of RNA Secondary Structure Motifs.
  • Vanegas, P. L., Hudson, G. A., Davis, A. R., Kelly, S. C., Kirkpatrick, C. C., and Znosko, B. M. (2012) RNA CoSSMos: Characterization of Secondary Structure Motifs- a searchable database of secondary structure motifs in RNA three-dimensional structures, Nucleic Acids D439-D444.