Multipe Sequence Alignments:
Using The T-Coffee Webserver
Open the the T-Coffee web server www.tcoffee.org
Carry out the following tasks:
- Align the following sequences using the T-Coffee regular mode.
- Try to make sense of the output. Do you think your alignment is correct.
- Use the T-Coffee advanced mode to select a specific output or change the selected methods.
- Use the Expresso Mode. Do you see any improvement?
- What are the structural templates that were used by Expresso.
- Use the M-Coffee mode to align your sequences. Switch to the advanced mode to change the selected methods
- Do you think the MSA methods are producing consistent alignments?
- 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
- Why does the M-Coffee alignment 'look' better that the Expresso?
- Try to get a better Expresso alignment
Questions should be sent to C.Notredame