Procedure

1. Open the simulator window. Read the general instructions on how to use this tool before starting the simulation.

 

2. To start the experiment, users can enter the DNA sequence of interest. They can also change the k-mer size by clicking the K-mer size box in the simulator window.

 

3. To practice the simulator, instead of step 2, users can download a sample DNA file in FASTA format provided in the GUI.

 

4. Then upload the downloaded file (DNA sequence) by clicking Choose file menu.

 

5. When the file is chosen, the DNA sequence gets entered in the text box.

 

6. Then click on start analysis to visualize the result. Read the basics of the De-Bruijn graph in the box provided in the simulator window.

 

7. The input details are displayed in the GUI. Read and understand the input details.

 

8. Next click on the Generate K mers tab.

 

9. The k-mers and its suffix and prefix gets displayed in the simulator window. Users can scroll the window to observe all the k mers and associated suffix and prefix.

 

10. Click on the Show only K-mers button to visualize the k-mers.

 

11. Click on Show Graph Construct button to observe the nodes. Users can scroll down to observe the list.

 

12. Click on Visualize Graph button to observe De- Bruijn graph.

 

Here the nodes represent (k−1)-mers, and edges represent k-mers.

 

13. Users can click on the rearrange button to observed re-arranged version of the De Bruijn graph.

 

14. Click on the reset button to re-start the experiment.

 

15. Click on the Export Result button to get the step-wise construction of the graph and de-Bruijn graph of the provided input sequence.