Tutorial

Coevolution analysis of the E.coli GroEL protein

1. Input consists of a set of 12 bacterial GroEL DNA sequences that have been aligned with clustalw: groel.aln (CAPS can process both DNA and protein sequences).
2. Browse to the CAPS Server home page and click on the 'Analysis' tab.
3. Instead of uploading the groel file you can simply tick the checkbox in the input section:

   

4. Click to open up additional input options:

   

5. Click on the link to transfer the PDB ID into the according text box:

   

   This will generate a 3-D image indicating the positions of co-evolving sites.

6. Additional parameter settings can be seen by clicking on the link in the Parameter section:

   

7. In this example the settings are made more stringent to reduce the number of false positives:

   

8. Scroll to the bottom of the page and click on the 'send' button:

   

9. A page indicating the submission status appears. This can be bookmarked.

   

10. After a couple of minutes the results appear:

    

11. You can interact with the cytoscape network by selecting and dragging nodes representing aminoacids, or using the control panel:

    

12. Below the network you can find a 3-D image of the protein:

    

    This shows a structural image of the E.coli GroEL protein. Co-evolving amino acids are indicated as green balls.

13. The table below 3-D image lists the various groups.

    

14. Select one of these to highlight only the associated sites:

    

15. Additional files can be downloaded to see the full text-based output:

    

16. See here for full results: Caps output for GroEL alignment