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DNA Strider Manual: Bio312 2000
Bonnie K. Baxter, Lewis & Clark College

When you're done exploring for a while, choose the enz menu option "graphic map." You should get a new window that looks something like this:

Notice that this map shows the name of the plasmid and its overall size as well as the presence of unique restriction sites, which are indicated by the name of the restriction enzyme and the position of the site (in basepairs, beginning from an arbitrary point numbered "1". In this case, "1" corresponds to the T7 transcription start site.)

This map shows only unique restriction sites--sites for enzymes that cut the plasmid only once. You may wish to use enzymes that cut the plasmid more than once, however. To see a map that shows this, go back to the main sequence window (click on this window to make it active), and then go up to the enz menu again. The option just under "graphic map" is "sites." Move the mouse to this option, and you should see a menu with the following options:

Choose "triple," and then go back and select "graphic map" again. You should get a new map which shows the sites for enzymes that cut 1, 2, or 3 times. There is a bolded number by each enzyme name that shows how many times that enzyme cuts.

Your graphic map will be circular if Strider thinks that your sequence is circular. Otherwise it will be linear. If your map turns out to be linear instead of circular or vice versa, here's how to fix that problem.

Click on the main sequence window to make it active. Now select the following option from the menu bar:

If the option "circularize" is checked, Strider thinks your sequence is circular. Select this option to toggle "circular" on or off. Then create a new graphic map as described above.

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