Last modified on 25 January 2016.

Literature Reference:

Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.
PM | PMC | DOI ]

Use RNA2DMap:

Manuscript Figures:

Description Figure
Figure 1: Overview of the RNA2DMap interface. PNG
Figure 2: Highlighting the selected base pair groups and their conformations. PNG
Figure 3: Five motif types are highlighted in different colors. PNG
Figure 4: (left) 3D distances are highlighted with a color map; (right) The conservation view of the 16S rRNA secondary structure. PNG
Figure 5:
  1. (Top) Most frequent base pair groups and conformations.
  2. (Bottom) Least frequent base pair groups and conformations.
Figure 6: Tertiary interactions between nucleotides in the tetraloop, lone-pair tri-loop, and the UAA/GAN motifs and its partner are drawn with a thicker line in RNA2DMap. Blue lines for base-base interactions and green lines for base-backbone interactions. PNG
Figure 7: The secondary structural map of T. thermophilus 16S rRNA highlights all neighbor effects (red lines connecting nucleotides). PNG