If required, you can select a subset of the available enzymes from the file you are using. Before you perform the analysis, open the restriction enzyme file and click in front of the name of any enzyme you want to select. A check mark appears to mark your choice. If you save the restriction enzyme file, the selections are saved with the file.
1. Make the required nucleic acid sequence window active.
2. Specify whether to analyze the sequence as a circular or linear molecule by clicking the linear/circular icon in the toolbar until it is set correctly for your sequence.
3. Choose Analyze | Restriction Enzyme.
4. Select Enzyme File to choose the restriction enzyme file that will be used for the analysis.
A file selection dialog box is displayed, enabling you to choose the file.
5. Choose the required file from the scrolling list and select Choose.
6. You can restrict the search to a certain region of the sequence by typing in the base numbers that bracket the region in the Region panel, or by selecting a region from the features table drop-down menu at the right of the text boxes.
7. Select your search criteria by choosing from the Search Using drop-down menu as follows:
- choose all enzymes to use all the enzymes in the selected enzyme file
- choose selected enzymes to use only the enzymes that you have selected within the enzyme file
- choose other criteria to display further options.
NOTE: When the other criteria search is performed, all enzymes in the file are used, not only the selected ones.
8. If you have chosen other criteria, do one or more of the following:
- to restrict the search to enzymes whose recognition sites are a certain size, type the size limits into the site size text boxes. MacVector accepts values from 1 to 100. Leave both boxes empty if you do not want to restrict the search by site size
- to limit the search to enzymes that leave 5' ends, 3' ends, or blunt ends when they cut the sequence, select the appropriate option from the end structure drop-down menu
- to restrict the search to enzymes that cut the sequence a limited number of times, type the upper limit in the number of cuts text box. MacVector accepts values from 1 to 20. Leave the text box empty if you do not want to restrict the search by number of cuts.
9. Select OK to perform the analysis.
When the analysis is completed, the Restriction Enzyme Analysis Display dialog box is displayed. This is used to filter restriction site search results as follows:
- by the number of cuts an enzyme makes
- by the end structure of cut fragments
- by restriction site size
- by the residue range in which the cut site occurs.
See the Filtering restriction site results help topic for further information.
Automatic Restriction Enzyme Analysis