To create restriction maps in GeneQuest, apply the Enzymes – Restriction Map method to the Assay Document. Use the Microscope tool to view restriction sites on an expanded portion of the sequence.
The following video shows the method in use:
Once you have applied the Enzymes – Restriction Map method, you can do any of the following:
| Task | How To |
|---|---|
| Display a table of restriction analysis results for Enzymes – Restriction Map methods applied to the Assay Document | Choose Sites & Features > Restriction Fragment Summary. The restriction enzymes selected from the Assay Document will appear in the tabular summary. If none are selected, then all will appear in the tabular summary. The summary lists the following data for single, double, and triple digests; the number and position of cuts; the enzyme responsible for each cut; and the length of the fragment. To change the parameters for this method, use Options > Fragment Summary Options. |
| View the predicted electrophoretic separation of restriction fragments through an agarose gel | Hold down the Shift key while you use the object selector to select the desired enzyme plots. When the appropriate enzymes have been highlighted, choose Sites & Features > Agarose Gel Simulation. While viewing the simulated gel, you may move the cursor over any fragment to display a header showing its range, size, and the restriction enzymes cutting each end. The far left and far right lanes are molecular size standards from bacteriophage lambda. The other lanes show all possible combinations of single, double and triple digests. Above each lane is the name of the enzyme(s) or molecular size standard. If you move the cursor over a fragment in the simulated gel, the header displays its range, size, and the restriction enzymes cutting each end. Fragments in red represent fragments within the current range selected in the assay document. You can change the selected range by double clicking on any DNA fragment in the gel simulation. |
| Toggle between treating a sequence as linear or circular | Choose Sites & Features > Linearize Sequence to treat the sequence as linear. Choose the command again to treat the sequence as circular. The ability to linearize sequences is especially important in restriction site analysis, since GeneQuest may find fewer cut sites on a linear strand than on a circular one. |
| Toggle between searching for restriction sites inside or both inside & outside the specified sequence sub-range | Choose Sites & Features > Sub-range Context to search both inside and outside the specified sequence subrange. Use the command again to restrict the search to the portion within the subrange. Note that this option does nothing unless you have previously used Set Ends to specify a sub-range of a sequence. |
| Toggle between including or not including ambiguous DNA residues when searching for restriction sites | Choose Sites & Features > Include Uncertain Sites to include ambiguous bases when searching for restriction sites. Use the command again to look only for literal matches. Example: When this option is active (i.e. checked), the sequence ANGCTT, an uncertain site for HindIII (AAGCTT), would be labeled as a cut site. |
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