Restriction Site Analysis

Besides the dynamic restriction sites, you can do a more elaborate restriction map analysis with more output format using the Toolbox:

        Toolbox | Molecular Biology Tools (Image lab_work_support) | Cloning (Image cloningandrestrictionsites)| Restriction Site Analysis (Image restriction_site)

You first specify which sequence should be used for the analysis. Then define which enzymes to use as basis for finding restriction sites on the sequence (see Manage enzymes).

In the next dialog, you can use the checkboxes so that the output of the restriction map analysis only include restriction enzymes which cut the sequence a specific number of times (figure 23.10).

Image restrictionstep3
Figure 23.10: Selecting number of cut sites.

The default setting is to include the enzymes which cut the sequence one or two times, but you can use the checkboxes to perform very specific searches for restriction sites, for example to find enzymes which do not cut the sequence, or enzymes cutting exactly twice.

The Result handling dialog (figure 23.11) lets you specify how the result of the restriction map analysis should be presented.

Image restrictionstep4
Figure 23.11: Choosing to add restriction sites as annotations or creating a restriction map.

Add restriction sites as annotations to sequence(s)

. This option makes it possible to see the restriction sites on the sequence (see figure 23.12) and save the annotations for later use.

Image restrictionsiteannotations
Figure 23.12: The result of the restriction analysis shown as annotations.

Create restriction map

. When a restriction map is created, it can be shown in three different ways: