Multiple Sequence Alignment – Exercise

We will use CLUSTALW to produce a multiple sequence alignment of the sequences we
collected during the last lesson.
• Locate the CLUSTALW start page at EBI
• Open the sequence file and copy and paste the sequences you want to align into
the respective field on the CLUSTALW page (make sure the sequences are in the
FASTA format)
• Use the default settings and click on RUN
• In the results window, click on ‘Show Colors’ to color the residues according to
the following table:

For table look in the help menu.

Save the alignment file
• Click on ‘View Guide Tree’ to display the Cladogram
• Show the distances
• Display it as a Phylogram and save an image of it (you will need to use the ‘print
screen’ function of Windows and some imaging software)
• Go back to the main results and start Jalview
Jalview is a multiple alignment editor written in Java. It allows for viewing and editing
MSAs as well as analyis and annotation of sequences using web services. Jalview is
available for free download.
• Locate the Jalview home page and run the software as a Java web-start
application. Now we can use it also for other outputs.
• As a first exercise, open the alignment file you saved from the CLUSTALW MSA
• Save the consensus sequence to a text file
Now we are going to use the MUSCLE program to align our sequences.
• Prepare a file containing the sequences in FASTA format
• Locate the MUSCLE web site and upload the file
• Run the algorithm and save the file in FASTA format
• Open the FASTA file in Jalview and compare both alignments
• Repeat the procedure with the respective DNA sequences

Result: Contact Jitendra Narayan