Multipe Sequence Alignments:
Using The T-Coffee Webserver

Open the the T-Coffee web server www.tcoffee.org

Carry out the following tasks:

1. Align the following sequences using the T-Coffee regular mode.
2. Try to make sense of the output. Do you think your alignment is correct.
3. Use the T-Coffee advanced mode to select a specific output or change the selected methods.
4. Use the Expresso Mode. Do you see any improvement?
5. What are the structural templates that were used by Expresso.
6. Use the M-Coffee mode to align your sequences. Switch to the advanced mode to change the selected methods
7. Do you think the MSA methods are producing consistent alignments?
8. Of all the alignments you have been producing, which one do you believe to be the most accurate for the two structures? The reference structural alignment is here
9. Why does the M-Coffee alignment 'look' better that the Expresso?
10. Try to get a better Expresso alignment