Link Variants to 3D Protein Structure

This tool makes it possible to visualize variant consequences on 3D protein structures. It takes a variant track as input, and produces a new variant track as output, with two additional columns in the table view:

In The variant table output it is described how to interpret the output in the variant table and how the tool finds appropriate protein structures to use for the visualizations, and in Create 3D visualization of variant and onwards it is described how the 3D models and visualizations are created.

Note: Before running the tool, a protein structure sequence database must be downloaded and installed using the Download 3D Protein Structure Database tool (see see Download 3D Protein Structure Database).

To run the tool, select:

        Toolbox | Resequencing Analysis (Image resequencing) | Functional Consequences (Image functional_cons_folder_closed_16_h_p) | Link Variants to 3D Protein Structure (Image variantsin3d_16_n_p)

If you are connected to a server, you will first be asked where you want to run the analysis. In the next wizard step you will be asked for an input file. The Link Variants to 3D Protein Structure accepts variant tracks as input (see figure 32.31).

Image linkvariants_proteinstructure_step2
Figure 32.31: Select the variant track holding the variants that you would like to visualize on 3D protein structures.

Click Next. In the next wizard step, you must provide a CDS track and the reference sequence track (figure 32.32).

If you have not already downloaded a CDS and a reference sequence track, this can be done using the Reference Data Manager (see Download Genomes).

Image linkvariants_proteinstructure_step3
Figure 32.32: Select CDS and reference sequence.

Click Next, choose where you would like to save the data, and click on the button labeled Finish.

As output, the tool produces a new variant track, with two additional columns in the table view ('Link to 3D protein structure' and 'Effect on drug binding site' - figure 32.33). The default output view is the variant track. To shift to table view, click on the table icon found in the lower left corner of the View Area.

Image linkvariants_proteinstructure_output
Figure 32.33: The variant table output.