In this section of the tutorial, you will learn how to search databases for a specific protein sequence. You will be working with the sequence that encodes the Replicase protein and a few others of the SARS virus. Notice the scrollable textbox on the page that contains a variety of tools. You will use some of these tools within this tutorial.

Importing Sequences from Protein Sequence Databases

1. Highlight "Ndjinn ¡V Multiple Database Search"and then click Run.


2. The next screen lists the different databases that you can search. In the search box at the top of the page type: SARS. This tells the search engine what to search for. Also, when searching, you are able to control the amount of results you get. Notice the "Hits per page" drop-down menu. This simply lets you decide how many sequences you want to display on the results page. To improve your choices, select "All".


3. As you scroll down the page, you will notice a list of different databases. They all contain a variety of sequences that you can search for. They are separated into 2 distinct groups: The first group contains sequences from many different organisms (for example, database "GBBCT" contains a large number of sequences from many different bacteria), whereas the second group contains the entire DNA genome sequences of specific organisms (for example, "Aaeo" contains the entire genome sequence of the bacterium Aquifex aeolicus) Since you are looking for a viral protein, click on the box that is next to the SWISSPROT database. This is a large database filled with many different protein sequences from many different organisms.


4. Scroll back up to the top of the screen and click "Search". You will then be sent to a page that contains the results of your search. At the time this tutorial was written, the search engine found 49 matches for "SARS". If you get more then 49 results, do not panic. Inconsistencies in the number of search results can occur because new sequences are being added to the databases on a daily basis.

5. From the descriptions of the search results, we need to determine which one encodes a series of proteins including the Replicase protein. The sequence you want is "SWISSPROT:R1AB_CVHSA" (rank # 0). This is a specific sequence to a mutated SARS virus (known as a "strain"). There are minor differences between strains of SARS viruses.


6. Select this sequence and click on the "Import Sequence(s)" button at the bottom of the page. Your sequence will be transferred to the Protein Tools homepage.