Procedure

This procedure will analyze selected restriction sites for occurrence of their recognition site in a DNA sequence and send the result to the Output window.

1. Proceed to the selection of restriction enzymes in the Restriction Enzyme Window if necessary.

If the Restriction Enzyme Window is not open, the set of prototypes (all enzymes without isoschizomers) will be used.

2. Choose Analysis > Restriction Analysis in the main menu or Sequence Analysis > Restriction Analysis in the selection contextual menu.

A sequence must be selected prior to operate a restriction analysis, e.g. click Ctrl-A to selected all the nucleotides in the sequence viewer first.

3. Choose any of listing options:

• All Sites: Report all sites found.

• Unique Sites: Report only sites that cut once.

• Absent Sites: Report sites that do not cut.

4. Alternatively click on the All Sites button (), or the Unique Sites button (), or the Absent Sites button () in the Restriction Enzyme Window operation toolbar. If the button is not active, reselect the sequence or activate the window containing the sequence, like for example a sequence node in the Explorer Window, before clicking in the toolbar.

5. Open the Output multitab window to access the result.

Example of output

The following report was generated by cutting the IgG4 Fc by all enzymes with a cutting size of 7 nucleotides or more using the All Sites option:

      IgG4_FC  •  All Restriction Sites
      DNA      768 bp   ATGAAAAAGACA ... CCGGGTAAATGA
      Number of restriction enzymes tested: 25
      
      Enzyme    Site                      Nb     Position  Strand  Isoschizomers
      AarI      CACCTGC(4/8)              1           668  -       
      SapI      GCTCTTC(1/4)              1           738  -       BspQI LguI PciSI
      PpiI      (7/12)GAACNNNNNCTC(13/8)  2           238  -       
                                          2           684          
      
      Absent Sites:
      AbsI, AjuI, AloI, AscI, BarI, BbvCI, CspCI, FseI, FspAI, MauBI, MreI, NotI,
      PacI, PmeI, PsrI, SfiI, SgfI, SgrAI, SgrDI, SrfI, Sse8387I, SwaI.