Procedure

This procedure will analyze the number of occurrences of restriction sites 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 > Site Usage in the main menu or Sequence Analysis > Restriction Analysis > Site Usage 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. Alternatively click on the Site Usage 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.

4. 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:

       IgG4_FC  •  Site Usage
       DNA      768 bp   atgaaaaagaca ... ccgggtaaatga
       Number of restriction enzymes tested: 25
       
       AarI          1  AbsI          -  AjuI          -  AloI          -  BarI          -  BbvCI         -  
       CciNI         -  CspCI         -  FspAI         -  MauBI         -  MreI          -  MssI          -  
       PacI          -  PalAI         -  PciSI         1  PpiI          2  PsrI          -  RigI          -  
       SdaI          -  SfaAI         -  SfiI          -  SgrAI         -  SgrDI         -  SrfI          -  
       SwaI          -