Show enzymes cutting inside/outside selection

Manage enzymes describes how to add more enzymes to the list in the Side Panel based on the name of the enzyme, overhang, methylation sensitivity etc. However, you will often find yourself in a situation where you need a more sophisticated and explorative approach.

An illustrative example: you have a selection on a sequence, and you wish to find enzymes cutting within the selection, but not outside. This problem often arises during design of cloning experiments. In this case, you do not know the name of the enzyme, so you want the Workbench to find the enzymes for you:

        right-click the selection | Show Enzymes Cutting Inside/Outside Selection (Image add_enzymes_cutting_selection)

This will display the dialog shown in figure 19.35 where you can specify which enzymes should initially be considered.

Image inside_outside_step1_web
Figure 19.35: Choosing enzymes to be considered.

At the top, you can choose to Use existing enzyme list. Clicking this option lets you select an enzyme list which is stored in the Navigation Area. See section Restriction enzyme list for more about creating and modifying enzyme lists.

Below there are two panels:

Select enzymes in the left side panel and add them to the right panel by double-clicking or clicking the Add button (Image add). If you e.g. wish to use EcoRV and BamHI, select these two enzymes and add them to the right side panel.

If you wish to use all the enzymes in the list:

        Click in the panel to the left | press Ctrl + A (Image command_key_web + A on Mac) | Add (Image add)

The enzymes can be sorted by clicking the column headings, i.e. Name, Overhang, Methylation or Popularity. This is particularly useful if you wish to use enzymes which produce e.g. a 3' overhang. In this case, you can sort the list by clicking the Overhang column heading, and all the enzymes producing 3' overhangs will be listed together for easy selection.

When looking for a specific enzyme, it is easier to use the Filter. If you wish to find e.g. HindIII sites, simply type HindIII into the filter, and the list of enzymes will shrink automatically to only include the HindIII enzyme. This can also be used to only show enzymes producing e.g. a 3' overhang as shown in figure 19.51.

Image restrictionstep2_web
Figure 19.36: Selecting enzymes.

If you need more detailed information and filtering of the enzymes, either place your mouse cursor on an enzyme for one second to display additional information (see figure 19.52), or use the view of enzyme lists (see Restriction enzyme list).

Image restrictionstep2_tooltip
Figure 19.37: Showing additional information about an enzyme like recognition sequence or a list of commercial vendors.

Clicking Next will show the dialog in figure 19.38.

Image inside_outside_step2_web
Figure 19.38: Deciding number of cut sites inside and outside the selection.

At the top of the dialog, you see the selected region, and below are two panels:

These panels offer a lot of flexibility for combining number of cut sites inside and outside the selection, respectively. To give a hint of how many enzymes will be added based on the combination of cut sites, the preview panel at the bottom lists the enzymes which will be added when you click Finish. Note that this list is dynamically updated when you change the number of cut sites. The enzymes shown in brackets [] are enzymes which are already present in the Side Panel.

If you have selected more than one region on the sequence (using Ctrl or Image command_key_web ), they will be treated as individual regions. This means that the criteria for cut sites apply to each region.


... available19.4
The CLC Genomics Workbench comes with a standard set of enzymes based on You can customize the enzyme database for your installation, see Restriction enzymes database configuration