How do we compare?

RNA Visualization Software



RiboSketch

  • Lu, J. & Bindewald, E.


NAVRNA

  • Bailly, G.; Nigay, L. & Auber, D. "NAVRNA: visualization - exploration - editing of RNA" Proceedings of the working conference on Advanced visual interfaces, 2006, pp. 504-507M


RnaMLView

  • Yang, H.; Jossinet, F.; Leontis, N.; Chen, L.; Westbrook, J.; Berman, H. & Westhof, E. "Tools for the automatic identification and classification of RNA base pairs," Nucleic Acids Research, 2003, 31, 3450-3460


RnaViz

  • Rijk, P.D. & Wachter, R.D. "RnaViz, a program for the visualization of RNA secondary structure," Nucleic Acids Research, 1997, 25, 4679 - 4684
  • Rijk, P.D.; Wuyts, J. & Wachter, R.D. "RnaViz 2: an improved representation of RNA secondary structure," Bioinformatics, 2003, 19, 299-300




RNA Visualization Software Capable of Pseudoknot Visualization



Forna

  • Kerpedjiev P, Hammer S, Hofacker IL . "Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams." Bioinformatics, 2015, 31(20):3377-9


PseudoViewer

  • Han, K.; Lee, Y. & Kim, W. "PseudoViewer: automatic visualization of RNA pseudoknots," Bioinformatics, 2002, 18, S321-S328
  • Han, K. & Byun, Y. "PseudoViewer 2: visualization of RNA pseudoknots of any type," Nucleic Acids Research, 2003, 31
  • Yanga Byun, Kyungsook Han; "PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures," Nucleic Acids Research, 2006, Volume 34, Issue suppl_2, 1, pp. W416–W422
  • Yanga Byun, Kyungsook Han; "PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots," Bioinformatics, 2009, 25(11), pp. 1435–1437


VARNA

  • Kévin Darty, Alain Denise and Yann Ponty. "VARNA: Interactive drawing and editing of the RNA secondary structure" Bioinformatics, 2009, 25(15) pp. 1974-1975


XRna

  • Weiser B, Noller HF. "XRNA: Auto-interactive program for modeling RNA. The Center for Molecular Biology of RNA, University of California, Santa Cruz




RNA Folding Software and Algorithms



RnaPredict

  • Wiese, Kay C. and Hendriks, Andrew (2009). "RNA Pseudoknot Prediction via an Evolutionary Algorithm," IEEE Congress on Evolutionary Computation (IEEE CEC ‘09), Trondheim, Norway, 270 – 276.
  • Wiese, Kay C., Deschênes, Alain, and Hendriks, Andrew (2008). “RnaPredict - An Evolutionary Algorithm for RNA Secondary Structure Prediction”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5(1), pp. 25-41


SARNA-Predict

  • Tsang, Herbert and Wiese, Kay C. (2015), “A Permutation Based Simulated Annealing Algorithm to Predict Pseudoknotted RNA Secondary Structures”, International Journal of Bioinformatics Research and Applications, Vol. 11(5), pp. 375-396.
  • Tsang, Herbert and Wiese, Kay C. (2010). “SARNA-Predict - RNA Secondary Structure Prediction Using Permutation-based Simulated Annealing”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7 (4), pp. 727-740


MFold

  • Zuker, M. "Mfold web server for nucleic acid folding and hybridization prediction," Nucleic Acids Research, 2003, 31, 3406 - 3415
  • Mathews, D.H.; Sabina, J.; Zuker, M. & Turner, D.H. "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure ," Journal of Molecular Biology, 1999, 288, 911-940


RnaFold

  • Hofacker, I.L.; Fontana, W.; Stadler, P.F.; Bonhoeffer, L.S.; Tacker, M. & Schuster, P. "Fast Folding and Comparison of RNA Secondary Structures," Monatsh.Chem., 1994, 125, 167-188