PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures
Fig 2
Examples of the structures which have non-nested interactions involving canonical base pairs and non-canonical base pairs visualized by PseudoknotVisualizer are shown.
This figure illustrates examples from PDB IDs 7PTK [27] and 6T3R [28], both of which are large sequences exceeding 300 nucleotides in length, making them particularly challenging to analyze visually without computational assistance. Note that, as demonstrated in Fig 1, all structural elements were set to white prior to applying the PseudoknotVisualizer coloring operation for clarity. These visualizations were generated with annotator=RNAView and the option include_all, thereby including the non-nested interactions involving non-canonical base pairs. The color scheme is as follows: white represents unpaired bases; gray indicates paired bases including non-canonical base pairs in the core layer; red, blue, and green represent paired bases in non-nested layers 1, 2, and 3, respectively.