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Examples

Example 1: Visualization of SSU rRNA helices in RiboVision mode.

Example of SSU rRNA
SSU rRNA helices

Here, we demonstrate the mapping of RNA helices onto the SSU rRNA from ribosomal structure 7k00. To visualize the molecule in RiboVision mode, users should first select one or multiple phylogenetic groups of species of interest from the phylogenetic browser (bacteria). The server will generate the list of available alignments for the selected groups of species, and the user should select a desired RNA molecule class (here SSU-rRNA) and an available alignment (SSU). Upon completion of these selection steps, an alignment that matches the criteria will be generated and appear with the MSA viewer in the upper part of the Visualization panel. Users will then be guided to select the PDB entry to visualize the 3D structure of the desired RNA molecule. Once a PDB ID (7k00) is provided, users will be prompted to select the RNA chain. The list of RNA chains in the selected PDB will be automatically generated, and users should choose a chain matching that of the selected alignment (16S ribosomal RNA). Selection of a matching RNA chain triggers visualization of the RNA 3D structure in the Mol* applet located in the lower right part of the Visualization panel. This selection initiates a series of backend processes leading to the retrieval or generation of the 2D structure from the available template. It maps the sequence from the 3D structure onto a pre-loaded MSA object, interlinking the 1D, 2D, and 3D panels into interconnected RNA representations. Here we demonstrate the mapping of pre-computed data (RNA helices) onto 2D and 3D structural representations of the LSU. To visualize helical objects, users need to select "helix" tab from the Data menu of the 2D RNA Viewer. Upon selection, individual helices are colored distinctly, with color changes indicating helical boundaries. The number of helices can be retrieved by hovering the mouse over specific nucleotides. Helical information is also available in the CSV file, accessible by clicking the "Download mapped data" button in the Main Navigation panel.

Example 2: Visualization of RNase P in the demo user upload mode

RNase P
Demo of user upload

Here we demonstrate the utility of the User-upload mode by supplying a custom alignment and structure (for RNAseP) and the mapping of custom experimental data onto its structure. To visualize a custom molecule, users should switch to the “User upload” mode in the Main Navigation panel of RiboVision 2. Users will be prompted to upload a custom MSA (or a single sequence) file in Fasta format. Within the MSA provided for upload, all sequences within the custom alignment must have equal lengths (including gaps). The uploaded alignment will be automatically clustered by CD-Hit using a threshold of 90% sequence identity. This clustering ensures unbiased computation of evolutionary statistics (Shannon Entropy or Twin Cons).

After uploading the MSA, users are prompted to upload a custom 3D structure of an RNA molecule. In the current example, we use the PDB option to upload the 3D structure. To proceed with this option, we extracted a single RNA molecule (chain B) from the RNAseP complex 3q1q Reiter et al. and saved it as a PDB file before uploading it to RiboVision. Once the upload mode (PDB) is selected by clicking one of the two radio buttons in the Main Navigation panel, users are prompted to upload the 3D structure file. In the PDB mode, users are additionally required to upload a full (genomic) sequence, as many RNA structures contain unresolved nucleotides. The full sequence must be uploaded in Fasta format without gaps. Alternatively, the users may select CIF option to upload the 3D structure, and to uplaod the RNase P molecule in the CIF format, providing the value for entity ID to be '1'.

The upload of the 3D structure and sequence will automatically trigger generation of the 2D diagram. The secondary structure diagrams will contain base-pairing predicted by R2DT, as the server doesn't currently extract base pairing from 3D structures. Once all representations of the custom RNA molecule appear in the Visualization panel, users can map statistical data computed from the MSA, available in the Data menu of the RNA 2D Topology Viewer.

RiboVision 2 also supports the upload of custom data in User-upload mode. Here, we demonstrate mapping of user-supplied data by visualizing the nucleotide index of RNase P. The data are compiled in a CSV file with two columns (nucleotide residues and corresponding data with proper headers). The custom file is uploaded by selecting the “Download custom data” button in the Main Navigation panel. The data will be automatically converted to a viridis color palette based on the minimal and maximal values in the CSV file. Corresponding nucleotides will be simultaneously colored in the 2D and 3D viewers. The resulting representations can be saved individually from each applet.