New Tool Visualizes Cancer Data Mutations in Three Dimensions
Have you ever wanted to see the mutations you’ve identified in three dimensions (3D)? Perhaps you’ve tried generating 3D data visualizations but stopped because the work was tedious and took too much time. If so, CBIIT has a new tool, called 3DVizSNP, that may be able to help.
You do not need programming skills to use 3DVizSNP. You can download the Python-based tool from Github and run it locally without installing any additional software or databases. You also can access the tool through a new interactive website set up by CBIIT’s Digital Services and Solutions Branch.
3DVizSNP offers advantages over existing mutation visualization tools because it automates the steps needed to view a list of mutations in 3D. You upload a Variant Caller Format file and in minutes the program produces:
- an output table of tens to thousands of mutations. For each mutation, you’ll see the variant, the gene ID, the protein ID, the structure ID, and predictions on whether the mutation is deleterious or not. You can sort and filter the table and download the results in csv format for loading into Excel.
- a visualization of the selected mutation in the iCn3D viewer (developed by the National Center for Biotechnology Institute’s Dr. Jiyao Wang). iCn3D allows you to toggle back-and-forth between the wild-type (or normal) and mutant (or changed) amino acids and includes annotations and links to other databases for information about the protein.
You’ll find the tool helps bridge the gap between genetics and structural biology so you can quickly and accurately visualize mutations in 3D.