Domain driver Mutation Estimator (DOME)

DOME execution

For running any script pertaining to DOME, make sure that the domeenv Conda environment is activated. More information about Conda environments can be found here

Running DOME command line (CLI) mode

The required scripts to run DOME are placed in the “script” directory.

To run DOME as a command line program, use the following commane: In Linux terminal:

$ conda activate domeenv
$ cd DOME-main/scripts
$ python3 <input_csv>

Format of the above mentioned "input_csv" should be as shown below. The CSV format file should contain 3 columns (column 1 - uniprot entry name of the protein; column 2 - amino acid position; column 3 - ALTERED amino acid) and may contain multiple rows (user defined). An example of the file contents is shown below :


Running DOME-GUI

To load the R Shiny based GUI or via web-browser use the following command:

In Linux terminal:

$ conda activate domeenv
$ R -e "shiny::runApp('app.R', launch.browser = TRUE)"

In Windows CMD:

> "Path/to/R.exe" -e "shiny::runApp("app.R", launch.browser = TRUE)"


Once users executes the above commands DOME GUI appears. DOME-GUI can be used for multiple queries (as in case of CLI mode) or explore individual protein positions.

Following are the detailed description for each of the tabs-

  1. For multiple queries - user may load the input file (in the CSV format shown above) and upon clicking "Submit", the results would be presented in a tabular Format as shown in below:


  2. For individual protein queries - user may input the protein name (Uniprot entry name), position (range with start and end position) and the results for the prediction would be presented in a tabular Format as shown in below:

DOME output

Gene based or mutation (position) based search returns a table containing the following columns:

Column namesDescription
Entry name Entry name of protein as per Uniprot database
Position Amino acid position in the protein
Reference Reference amino acid in the protein
Altered Altered amino acid in the protein
Domain Domain name
Mutation typeH - hotspot, R - resistant, '-' - not present in significant mutation database
Analogous toQuery protein position is analogous to this known significant mutation
DOME ScoreScore computed using the DOME algorithm scoring metric (scaled 0-1)