Exercise 4 - Multiple Sequence Alignment

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

1- Align insulin sequences

We will use a version of CLUSTAL locally installed on your computers. The steps required to align the sequences are the following:

Start the ClustalX : open a command shell, and type: clustalx
Load the insulin sequences from vertebrates you saved on your computer during Exercise 3 with the Load Sequences option from the File menu.
Start the alignment computation by selecting the Do Complete Alignment from the Alignment menu.
Confirm that you will use the default names used to store the alignment and the guide tree files produced by CLUSTAL by clicking on the ALIGN button.

2- Look at the alignement and save it

Start the SeaView program: type seaview in the command shell. Now load the alignment produced by ClustalX with the Open Clustal option from the File menu. Then, the first thing to do is to save that file in a format usable by the Phylo_win program (we will need it in Exercise 5). To do that, use the Save as... option of the File menu. Give to the saved file a name with the extension .mase in a way to differenciate it from the file generated by ClustalX.

3- Sequences conservation and domains

Now, check the position of insulin chains A, B and peptide C in the alignement: compare the sequence conservation of the three domains among species. What can you say?

4- SeaView use to alignment editing

See how you can use SeaView to edit the alignment.

If you have problems or comments...

Back to PBIL home page