However, the most useful way to access sequences is to use our brand-new tool "Sequence Server." To
use this tool, you will need access to the internet and either Netscape 4.0 (or better) or Internet Explorer 4.0 (or better).
The tool is at http://www.dnalc.org/sequences/.
After logging in to Sequence Server, you should click the "Manage Groups"
button at the top of the screen. This will open the Manage Groups window. In this window, choose "Classes" from the popup menu on the upper-right. A new screen will appear, and you will be able to see your class's name in the list presented. To select your class. Click on the checkbox next to your class, and click the OK button. This will put your class on your worksheet.
To compare sequences, you need to have more than one sequence on the worksheet. To add a sequence, select the desired sequence from the popup menu at the bottom of your class. Do this for as many sequences as you want. Then, click the checkbox for each sequence you wish to include in a comparison, then click on the "Compare" button. Sequence Server will open a new window showing the results of your analysis.
To find related sequences in Genbank, click the right radio button for the sequence you wish to search with, then click on the "Analyze" button. Sequence Server will open a new window showing the results of your analysis.
You can also use sequence server to examine the sequences in our database (by clicking the "Manage Groups" button), search GenBank for any sequence matching a keyword (by clicking the "Search by Keyword" button), and to type in your own sequences (by clicking the "Create Sequence" button).
1. First, look at your sequence. Sequence quality is analyzed by length of product and by the percentage of NŐs (unidentified bases) in the sequence. Discuss these parameters as they pertain to your sequence.
2. If you can, download the trace file. You may need to follow the directions to obtain an additional plug-in to see the file. Using this file, can you determine the identity of any of the bases the computer deemed ŇNÓ? Go back to the initial sequence window and change any bases necessary.
3. Now, compare your sequence to at least 2 other class members. Note that the dashes are placeholders, where one sequence has deletions as compared to another. Which sequence do you match the most? The least? Comment on the differences between your sequence and others in the class.
4. Find related sequences in Genbank, and compare your DNA to at least 4 other sequences. Explore different ethnic groups as well as hominids from different times. Which sequences are most related? Least? Comment.
5. Compare your sequence to others in the CSHL database. Comment on what you find.
6. Comment on the information such a sequence gives (or doesnŐt give!) How could these sequences be used to examine evolution and phylogenetic relatedness?