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| DOWNLOADING GENBANK PROTEIN SEQUENCES FOR YOUR CASE STUDY. |
| Dr. Kathy Takayama |
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| This is a step-by-step guide to using Biology Workbench to download Genbank protein sequences for your case study. |
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Procedure:
1. Activate your web browser (Netscape, Internet Explorer, etc.)
2. Go to the Biology Workbench Login Page at: http://workbench.sdsc.edu/
3. Log in with your username and password.
4. Once you have logged in, scroll down and click on the link button "Session Tools".
5. Highlight the selection: "Start New Session", and click on the link button "Run".
6. Under the "Session Description" type in a logical title that is relevant to the group of sequences you are downloading; for example: "Long-Term Non-Progressors, V3 region". Click on the link button, "Start New Session".
7. Click on the link button, "Protein Tools".
8. In the white box, highlight the selection: "Ndjiin - Multiple database search", and click on the link button, "Run".
9. Scroll down and tick the box "GBVRL" (Genbank Viral Sequences).
10. Type in the Genbank accession number for the viral sequences you wish to download. There are several ways you can do this. You may retrieve them one at a time, in which case you would highlight the option: "Exact Match" in the scroll down box. On the other hand, if you had a block of sequences that all began with the same six numbers, with the last number varying, you can highlight the option: "Begins With" and type in the block of six numbers. For example: "Begins With 391667" will retrieve all accession numbers from 3916670 - 3916679. If you think your strategy carefully, you may be able to avoid retrieving them one at a time. However, you want to make sure that you only retrieve the HIV-1 sequences that are in your case study; sometimes if you don’t define your block narrowly enough, you might end up with extra irrelevant sequences.
11. Leave the other options in their default settings, and click on the "Search" button.
12. Your search results should appear at the bottom of the window. Click on one of the sequences to select it, and click on the link: "Show Records". This will bring you to a page containing all of the relevant information for that sequence. You may wish to save or print the page for your own reference.
13. To import your sequences into your session: Click on one or more of the retrieved sequences in the window to select them, and then click on the "Import Sequence(s)" link.
14. Repeat steps 7 through 12 until you have imported all of your sequences.
15. Check your imported sequences to make sure you do not have duplicates. Delete duplicate sequences if you do.
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