Compare Tool

Overview of the Compare Tool 👓

To enable users to simply explore the differences between two subsets of our data on our servers, we have created an "Compare" tool ✨

This tool consists of two filter panels with many options for users to click through and choose which differences they want to see. The results are shown in an overview table (counts) as well as three separate tables for the subsets unique to each search category and the subset in common between the two chosen sets. All tables are easily downloadable.

Getting started

To showcase how to use the compare tool on an example, we are showing the steps on how to filter and use the compare tool for the example written in our paper manuscript (https://doi.org/10.1101/2023.02.03.526935).

1. Select the Compare tool

2. Filter panel

• A. Choose if you want to include only "complete genomes" in the next steps or both "complete and partial genomes" (term definitions: https://www.ncbi.nlm.nih.gov/assembly/help/). In our example, we chose both complete and partial genomes.

• B. Choose based on which reference genome you want to explore variants. In our example, we chose the reference genome: "MT903344.1".

• C. Choose which genes you want included. Here all are selected per default. In our example, we are interested only in relevant genes for the APOBEC3A gene, namely "MPXV-UK_P2-076", ”MPXV-UK_P2-182”, ”MPXV-UK_P2-157”. (This is the subset used in the paper, there are definitely more relevant genes one could filter for.) This can be done by unselecting all genes (click on the blue button next to "Select All"). Then you can press on the text field and type "MPXV-UK_P2-076" and click on the gene, and continue searching for the other genes.

• D. Choose which genes you want included. Here all are selected per default. If you want only one gene to look at, for example, the Gene "OPG210" with importance in the immune response (as mentioned in this paper: https://pubmed.ncbi.nlm.nih.gov/35906185/), we can unselect all genes, by clicking on the blue button next to "Select All". Then you can press on the text field and type "OPG210" and click on the gene.

**Note: The filters take effect as soon as you press them. There is no need for a submission of the request in any form.

Note: User can find more example queries with tooltips at "example command tab".

3. Once after clicking

The loading screen indicates that the query is currently processing and loading.

4. Table Output

Note: User can click export button to download the result.

5. Map Output

• Map will be updated when the table result gets an update.
• Map legends display mutations in accordance with their sizes.
• For more flexibility in map rendering, some mutations with frequencies less than a certain number are filtered out (please download the full result from the table for downstream analysis).