Tutorial

Coevolution analysis of the E.coli GroEL protein

  1. Input consists of the alignment of 12 bacterial GroEL DNA sequences that has been prepared: 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:

    Without a PDB file a stick-and-ball image will be generated.

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

  7. A page indicating the submission status appears. This can be bookmarked. After a couple of minutes the results appear:

  8. Click on the image to see a larger version:

    This shows a structural image of the E.coli GroEL protein. Beta sheets are coloured green and alpha helices in orange. Co-evolving amino acids are indicated by coloured circles and their position within the protein sequence.

  9. Additional files can be downloaded for the full text-based output:

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



kahokamp@tcd.ie