Aligning the Sequences: Using CLUSTALW
In order to compare the protein sequences, they must be aligned one on top of the other. This is the purpose of the CLUSTALW tool. The alignment process takes place by comparing the two sequences and finding common regions within them. Therefore, alignment is a key step for you to determine where differences in the sequences are located. The two sequences that you imported are aligned one on top of the other using colors that show you where similarities and differences exist.

1. Scroll down the textbox menu and highlight "CLUSTALW ¡V Multiple Sequence Alignment". Click no you two SARS virus sequences, SWISSPROT:R1AB_CVHSA and GBVRL:40457448_40457449. Then click on the "Run" button.


2. Another careen will appear in which alignment options can be altered- we are going to use the default settings so just click on the "Submit" button. You will now be taken to a screen that will show you the aligned sequences.

You will notice that in the middle of the alignment, there are dashes (- - - - -) for the sequence GBVRL:40457448_40457449. This is due to the fact that the scientists that submit sequences to the databases have been unable to determine the sequence of the protein at this spot. All amino acids in the sequences that are the same are colored bright blue. For the sake of this tutorial, all amino acids that are colored dark blue and green are very similar amino acids, but they ARE different. All amino acids that are colored black are not similar at all. These are the amino acids that cause there to be different strains of the SARS virus.


Using the various tools in the workbench, you have shown that different strains of the SARS virus are caused by small mutations (changes) in amino acids in protein sequences. What effect could this have on the proteins of different virus strains? In the next part of this tutorial, you will use a tool that will allow you to see a SARS protein in 3-D.