Finding another similar strain of SARS: Using BLASTP
Now that you have a strain of SARS, you can use it to find another similar strain of the virus. Because we know that the SARS sequence that you have found already has a similar sequence to other strains, we can use the original strain to search a database for sequences that are extremely similar (or homologous) to it. In order to do this, you are going to use a tool called BLASTP, more commonly called BLAST.

1. Scroll down the text box on the Protein Tools homepage and look for the tool called BLASTP ¡V Compare a PS to a PS DB". (This stands for "Compare a Protein Sequence to a Protein Sequence Database"). Select this tool and ensure that your SWISSPROT:R1AB_CVHSA protein sequence has a checkmark in the box next to it. Then click on the "Run" button.


2. You will next be sent to a screen that will give you many options. These options allow the user to specify their search. For the purposes of this tutorial you do not need to deal with this. The important step here is to choose the database that you want to use for your homology search. Scroll down in the text box until you come to the "GenBank Viral Sequences" database. Once again, you are only interested in the viral protein databases because you are dealing with viral sequences. Select "GenBank Viral Sequences" and then click on the "Submit" button at the bottom of the page.


3. You will be sent to the following screen that contains the results of your BLASTP search:


The first column after the description of the sequence is the "Score (bits)" column. You will see that the first sequences with Score (bits) values have very high ones. A Score (bits) value above 400 means that the sequence is very similar to the original sequence you compared it to. However, you can be more certain of the extent of the similarity between the two sequences by looking at the "E Value". This number is to the right of the "Score (bits)" value. Essentially, the smaller the E Value, the more similar the sequence is to the original sequence BLASTED. An E Value of zero represents a perfect or near perfect match.

As you can see, all the E Values shown are zero. This shows the high degree of similarity between different strains of the SARS virus. You will be able to see how similar each of them are later in the tutorial.

Now it is time to decide which strain sequence you want to use to compare to your original sequence. Since you know that different strains of SARS virus are very similar, you should expect them to be nearly identical (have very high homology). By reading the descriptions of the sequences, you notice that most of them say "[SARS coronavirus¡K]". This indicates that it is a SARS virus and the following code of letters indicates the specific strain.

4. You are able to find out more information about the sequences by checking the box next to the sequence and clicking the "Show Record(s)" button. Highlight the first few boxes and click "Show Record(s)". Notice that a detailed report is given to you for each sequence you highlighted.


For this tutorial we will be working with one of the strains found in Shanghai, China. If you are working in Internet Explorer, click on the "Back" button or, if you are working in Netscape, simply close the Records window (by clicking on the box in the top left-hand corner of the window). You should be back on the screen that contains the results of you BLASTP search. Make sure that only the Shanghai sequence (GBVRL:40457448_40457449) is highlighted.

5. Now scroll to the bottom of the screen and click on "Import Sequence(s)". Your Shanghai strain of SARS virus will be imported to the Protein Tools homepage.

Now you have two different strains of SARS virus sequences. You can compare and contrast the sequences. It is time to see where the differences lie in these two sequences.