In this section you will learn how to search sequence databases within the Biology Workbench for a DNA sequence and to store the results of that search on your session. 

Click to see a video demo of all the steps involved in this part of the exercise. In order to play the video, you should have flashplayer plugin installed. You can download the plugin from .

1.  Resume a Session. In Part I you created a session called Sickle Cell Anemia. We are ready to use it now.

            Open a web browser and go to the Biology Workbench http://workbench.sdsc.edu

            Log in to your account

            Select from the list of sessions, the one named Sickle Cell Anemia  

            Select from the window the line that reads Resume Session 

            Click the Run button, located just below the window

            Make sure that the session you selected is the active session by checking that the name displayed in the rectangle right below of the list of tools reads Sickle Cell Anemia

2.  Select Nucleic Tools.  We need to look for DNA sequences rather than amino acid sequences;  therefore we need to choose the  Nucleic Tools located across the screen close to the top of the page.

3.  Select the search program. The Biology Workbench allows you to perform a search on multiple databases at once; most of the databases are of sequences, however, there are also databases of scientific publications.

            Highlight Ndjinn - Multiple Database Search from the window

            Click the Run button

            A new window shows up with the title  Ndjinn - Multiple Database Search

4.  Formulate the search. As mentioned in the Introduction you will be working with the beta-globin gene in humans as this is where the mutation occurs that causes sickle cell anemia. Note that the Biology Workbench does not have a separate database for the human genome only, but it does have another database that contains such information, that is the GBPRI.

            Leave unchanged the first box that reads Contains

            In the next box type this text: beta globin

            Click  in the Hits per page pull down menu and choose All

            In the Display mode pull down menu do not change anything

            Scroll down the list of databases and select GBPRI GenBank Primate Sequences

            Click the Search button located below the window

5. Examining the results.  At the time this tutorial was being written, the search engine found 293 matches for “beta globin”.  If you get more than 293 results, do not panic. Different matches in the number of search results can occur because new sequences are being added to the databases on a daily basis. To examine the results, simply scroll down the list of results.

6. Selecting and importing the record of interest.  From the descriptions of the search results, we need to determine which one is the wild type sequence for beta globin.  The sequence you want is “gbpri:29436 - human messenger rna for beta-globin” (you may need to scroll down the results list to find this sequence and then copy it to your session with Import sequence).  Notice that the results of the search do not get automatically copied to your session; instead, you need to select from the results the one(s) you want to keep for future use and copy them to your session by executing the Import command on the selected results.

            Scroll down the list of results until you locate the line that reads

            gbpri:29436 - human messenger rna for beta-globin

            Select that line by click the box in front of it

            Scroll down to the bottom of the page and click on Import Sequence

            [The selected record will be copied to your session.

            You will be taken to the original Sickle Cell Anemia window and

            You should see the above  sequence in the list of data available to you]