Enzyme Selector Manager - User Guide to SeqBuilder Pro

The Enzyme Selector Manager is opened by choosing Enzymes > New Selector or Enzymes > Selector Manager.

This topic describes the layout of the Manager. Additional information about using the Manager is in the topic Create and manage sets of enzymes.

The Selector list on the left contains a list of all the selectors available for use. Choose a selector to modify by clicking it. The selector’s criteria will then appear in the Definition section of the dialog, and the enzymes that are included in this selector group appear in the Results section of the dialog (if this selector chooses any enzymes).

The Definition portion of the dialog contains the criteria that the selector uses for displaying specific enzymes using the Enzymes button tool ( ). This portion of the dialog contains the following items:

- Name contains the name of the current selector. You can enter a name for a new selector here when you wish to create a new selector.
- Type sets the type of selector and changes the options offered in this dialog. See the table below for details:

Type	Description
Class	To create a selector that uses class, complexity, availability (or some combination of these) as its criteria. Only precise – Check to select class II sites. Only random – Check to select class I sites. Check both boxes to select enzymes from either class. Site complexity – Check to limit the enzymes in this selector by the minimum length of the recognition sequence. Enter the minimum length in the Min box. Check the Range box if you wish to set a maximum length for the enzyme as well as a minimum length. Commercial – Check to limit the enzymes in this selector to those that are commercially available. On hand – Check to limit the enzymes in this selector to those that are currently available in the laboratory. To use this, each enzyme that is on hand should be so marked.
Overhang	To create a selector based on a set of overhang criteria. Overhang compatible with – Check to enable a drop-down menu that lets you specify whether the overhang be compatible with any enzyme or with one specific enzyme. Overhang length – To set a minimum length in base pairs for the overhang for either 3’ or 5’ overhangs. Set a range of base pairs by checking Range: The previous two options (Overhang compatible with and Overhang length) are mutually exclusive. Overhang degeneracy – Choose whether this selector should use only specific, only degenerate, or both types of enzymes.
Frequency	To create a selector based on criteria that specifies the frequency in which cutting sites appear within a specified range in the sequence. Use this also to find unique cloning sites or fragment exclusion sites. Cut frequency: To specify the frequency of cutting sites within a range. Check Range if you wish to specify a Min imum and Max imum number of cuts that fall within the range. Target sequence: To select a sequence other than the current sequence; either another open sequence, or another sequence stored on your computer. Click Browse to select another sequence from the hard drive Or use the drop-down menu to select a currently open sequence from the list. Generally, frequency filters should not have a specific target. To apply the filter to any sequence, do not browse to a specific sequence, but instead select <Set when applied> from the drop-down menu. The program will not evaluate the Result and display it on the right side of the window. Instead, the results will be evaluated when the selector is applied to the sequence. Sequence range: Check to specify the Begin ning and End of a sequence segment where this enzyme must cut the strand the number of times specified in Cut frequency.
Pick	To create a selector that only displays specific enzymes. To add an enzyme to the selector, click its name in Remaining Enzymes and click the left arrow. To remove an enzyme from the selector, click its name in Selected Enzymes and then click the right arrow.
Combine	To create a selector that is a combination of other selectors. Choose a selector in the center column list and then select a logical connector in the first column. You can choose not for the first selector to choose enzymes that are not in that selector. You can choose not, or, and, or not, or and not for the second and subsequent selectors. Click + to add another selector and another row to the selector list. Click – to remove a selector and a row from the selector list along with any associated logical connector.

The Results list on the right displays the enzymes that this selector will display on the sequence when chosen. Results cannot always be evaluated, so this section could potentially remain blank. In a case where the results cannot be evaluated, red text appears on the dialog explaining why the results can’t be evaluated. The buttons in this dialog are used as follows:

Type	Description
Evaluate	To apply new criteria to the selector. Enzymes that will be selected by this selector appear in the Results list on the right of the dialog. If the selector displays the desired set of enzymes in the Result box, click OK to save the Selector. There are some cases when the selector cannot be evaluated. You can create a Frequency filter where the Target Sequence is set to <Set When Applied>. In this case, the filter is not evaluated until the filter is actually applied to a specific sequence. This allows you to create a generic “unique” filter that will show only enzymes that cut a specific sequence one time. The set of enzymes will vary from sequence to sequence. Such selectors are not evaluated until applied to a sequence.
Revert	To remove all changes made to the current selector and revert to the original criteria. This option does not apply to changes made to the selector name or type.
New	To create a new selector.
Delete	To remove the selector.
OK	To accept any changes made since opening the Enzyme Selector Manager and return to SeqBuilder Pro. The new or modified selector will appear in the Restriction Enzymes > Selectors folder.
Cancel	To reject changes made since opening the Enzyme Selector Manager and return to SeqBuilder Pro. If you click Cancel when creating a new selector, the new selector will not be added to the Restriction Enzymes > Selectors folder.

Create and manage sets of enzymes

Try it! – Find restriction sites on either side of a feature

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