Enzymes – Restriction Map

This method identifies restriction sites and displays them as a mini-map, showing recognition sites as vertical bars. GeneQuest can also superimpose mini-maps to show restriction patterns from multiple digests. To view information about a particular enzyme, double click on its name in the Method Curtain or on its map display on the Assay Document to launch a text box that includes a list of isoschizomers, the enzyme recognition sequence, cut sites, site complexity rating, class (precise, random or unknown cutter), and vendor information, including cost/unit.

*Note: Restriction map functionality and useability is greatly improved in SeqBuilder Pro, our modern application that is installed alongside GeneQuest. To learn about working with enzymes in SeqBuilder Pro, click here.

For information on using this method, including a video demonstration, see Analyze restriction sites.

To change method parameters:

1. Double click on the method name in the Method Curtain; or select the method display and then Analysis > Method Parameters.

2. Choose whether you want to treat the sequence as Linear or Circular.

3. Check Examine Context at Ends of Sub-range if you are using a sequence sub-range for your assay. If checked, GeneQuest will examine 25bp upstream and downstream beyond your chosen coordinates. This will determine if any recognition sites located outside the range cut bases inside it.

4. Check Report Sites that Might Cut Degenerate Sequence to display sites with degenerate bases potentially cut by a given endonuclease. For example, Acc65I, which recognizes GGTACC, will recognize the degenerate sequence GRTACC only if this box is checked.

5. Choose a Selector from the list box to use a subset of restriction sites from an existing enzyme file. Selectors are created using DNASTAR’s SeqBuilder Pro application. Each selector will identify only the specific subset of sites specified by the selector.

6. Choose Show Filter Result from the Selector list to open a window that displays picked and remaining enzymes in the checked selector. You may double-click the name of any restriction site in that window or in the Method Curtain to view information regarding the enzyme’s recognition sequence, cut site, complexity, and other properties.