Creating and Editing Enzyme Boxes

To Create or Edit an 'Enzyme Box', select 'Edit Enzyme Boxes' from the Restriction Enzymes Menu. The Enzyme Box Editor Window is opened.



Creating, Editing and Deleting Enzyme Boxes
To Create a New Enzyme Box, press the 'New Box' button located on the 'Edit' buttons panel. To edit an existing Enzyme Box, select an enzyme box to edit using the 'Enzyme Box Selector' located at the top of the panel and edit the enzymes selected as describes below. To save changes introduced during editing, press the 'Save' button. To save the changes with a new name, select the 'SaveAs' button. To delete the current enzyme box, press the 'Delete' button.

Note that you cannot make changes to or delete the preset enzyme boxes.

Selecting Enzymes
Selected enzymes are shown in the selected enzymes table on the left of the editor, while available enzymes are shown in the panel on the right of the editor. Individual enzymes are selected or deselected by pressing the 'Selection CheckBox' to the side of each enzyme.

Groups of enzymes can be selected by pressing the group selection buttons

'Select All' selects all the available enzymes.
'Deselect All' deselects all the enzymes in the Box.
'Select Prototypes' Selects enzymes which REBASE defines as the prototype of a group of enzymes with identical specificity. If the prototype enzyme is not commercially available, another enzyme in the group is selected.
'Select Non-Degenerates' selects enzymes which do not recognise degenerate sequences such as AccI (GTMKCC)
'Dynamo' selects enzymes which after cleavage generate either a blunt end or a cohesive end which is not degenerate.
'Select Blunts' selects enzymes which generate a blunt end following cleavage
'Select 5'Overhangs' selects enzymes which generate 5' overhangs following cleavage
'Select 3'Overhangs' selects enzymes which generate 3' overhangs following cleavage
'Select' on the 'length' panel selects recognition sites whose length lies equal to or between the selected values. Note that degenerate bases do not contribute to the length of the site in this selection model
The 'Company' panel allows selection of enzymes sold by a particular company as defined by REBASE.

Combining Group Selections
Pressing a 'group selection button' selects all the appropriate enzymes from the list of all available enzymes. However, sometimes it may be desirable to select a further subset of enzymes from those which are already selected. You can do this by pressing the 'SHIFT' key on the keyboard at the same time as selecting a group button For example, to select Prototypes that aren't degenerate, first press 'Select Prototypes' then press 'SHIFT' and 'Select Non-Degenerates'.