Exercise 3: Multiple sequence alignment

Objective: compare vertebrate insulins to search for conserved domains in the proteins.
 

Step 1: Retrieve vertebrate insulin homologues with BLASTP. This time we will use another web server:  BLAST at PBIL ( *** ). Use default parameters.( *** )

Step 2: Filter BLAST output with the following parameters (button "Filter by taxon/keyword/date) ( *** ):

• Taxon is: vertebrates
• Keyword is not: partial

Step 3: Select (i.e. click on radio-buttons) all insulin (except those that are too short i.e. > 60 aa, and do not select INSULIN-LIKE GROWTH FACTORS), and then click on "Get selected sequences" ( *** ). Save the sequences as a TEXT file on your computer.
 

Step 4: Align sequence on your local computer with clustalx (default parameters)
 

Step 5: Look at the alignement with seaview.

NB: you first have to install these two software on your own computer (see http://pbil.univ-lyon1.fr/alignment.html for useful links. More help.

•  check the position of insulin chains A, B and peptide C in the alignement: compare the degree of sequence conservation of the 3 domains. What can you say ?
• see how you can use seaview to edit the alignment