Fig 1.
The secondary structure of the td group I intron pseudoknot (Accession ID: LC074723.1), with the different RNA structural motifs outlined.
Sequence taken from http://pseudoviewer.inha.ac.kr/, examples tab, and image produced utilizing jViz.RNA 4.0.
Fig 2.
The compressed and detailed graph representations for a sample RNA molecule.
(a) A sample RNA structure molecule. (b) The RNA molecule underlying representation used in RiboSketch [30] and Forna [31] (detailed graph). (c) The underlying representation of the RNA molecule in jViz.RNA 4.0 (compressed graph). (d) The representation also follows a tree structure where the first loop (which will always contain the 3’ and 5’ nucleotides) is the root, and the loops with only one stem attached to them always acting as leaves in the tree.
Table 1.
A comparison of the different RNA visualization software and their properties.
Fig 3.
After the automatic layout of the helper nodes (blue spheres) has been computed (center image), users can drag the helper nodes to manipulate the pseudoknotted base-pairs to either reduce space (right image), or expand a pseudoknot to draw attention or isolate its base-pairs (left image).
Fig 4.
The resulting visualization of the Beet Western-Yellow Virus pseudoknot, labeled [AB] by jViz.RNA 4.0 (EMBL number X13063) [33–35] responsible for viral frameshifting utilizing: (a) PseudoViewer 3 [23], (b) jViz.RNA 4.0, (c) VARNA [29], (d) Forna [31], and (e) RiboSketch [30].
Fig 5.
The resulting visualization of the T. thermophila pseudoknot, labeled [AB] by jViz.RNA 4.0 (EMBL number V01416) [36–38] ribozyme utilizing: (a) PseudoViewer 3 [23], (b) jViz.RNA 4.0, (c) VARNA [29], (d) Forna [31], and (e) RiboSketch [30].
Fig 6.
The resulting visualization for the td group I intron pseudoknot, labeled as [AB] by jViz.RNA 4.0.
Structure taken from http://pseudoviewer.inha.ac.kr/, examples tab (Accession ID: LC074723.1) images produced utilizing: (a) PseudoViewer 3 [23], (b) jViz.RNA 4.0, (c) VARNA [29], (d) Forna [31], and (e) RiboSketch [30].
Fig 7.
The resulting visualization of E. coli alpha pseudoknot, labeled [ABC] by jViz.RNA 4.0 (EMBL number X02543) [39] utilizing: (a) PseudoViewer 3 [23], (b) jViz.RNA 4.0, (c) VARNA [29], (d) Forna [31], and (e) RiboSketch [30].
Fig 8.
An example of the process involved in creating an RNA structure using jViz.RNA 4.0.
Users can feed the sequence into the software, and introduce base-pairs between the required bases. While not shown, users can also remove base-pairs as easily as they can add them.
Fig 9.
(a)-(b) A sample pseudoknotted structure which would be labeled [AB]. (c)-(d) A sample pseudoknotted structure which would be labeled [ABA]. (e)-(f) A sample pseudoknotted structure which would be labeled [ABC].
Fig 10.
A sample pseudoknotted structure (kissing hairpin) where base-pairs have been divided into A and B base-pairs.
Fig 11.
A sample visualization of the Beet Western-Yellow Virus pseudoknot (EMBL number X13063) using the novel method in jViz.RNA 4.0.
Main structure base-pairs are black while pseudoknotted base-pairs are pink.
Fig 12.
The nucleotides ni and nj, which are joined by a pseudoknot base-pair are used to determine the position of the midpoint .
The vector is then calculated, and rotated to produce
. The initial position of the helper node nh is then placed at
.
Fig 13.
The helper node (blue sphere) is capable of independent motion since it experiences repulsion forces (black arrows) from the loop nodes in the RNA structure, and attraction forces (red arrows) from the nucleotides it creates a pseudoknot arc with.
Fig 14.
(a) An example of a base-pair deletion where both adjacent nodes are base-pairs. (b) An example of a base-pair deletion where the child node is a loop while the parent node is a base-pair.
Fig 15.
(a) An example of a base-pair deletion where the parent node is a loop node while the child node is a base-pair. (b) An example of a base-pair deletion where both adjacent nodes are loops, resulting in a combined loop.
Fig 16.
(a) An example of a base-pair addition where only the parent of the resulting base-pair is a loop node. (b) An example of a base-pair addition where only the child node is a loop while the parent node is a base-pair.
Fig 17.
(a) An example of a base-pair addition which splits the loop node into two smaller loop nodes. (b) An example of a base-pair addition where both parent and child nodes are also base-pairs.