Restriction site detection

Restriction enzymes are a group of enzymes that can cut double-stranded DNA molecules into smaller restriction fragments. The enzymes work by cleaving the bonds in the phosphate backbone of the DNA molecule. These bonds can be reformed by ligase enzymes and in this manner restriction fragments with different origin can be spliced together in novel ways.

Restriction enzyme lists

When finding restriction sites, it is often an advantage to use a personalized and modified list of enzymes. This makes the analyses faster than using an extensive list. Also, the output of the restriction site finding is much easier to overview. Enzyme lists can be easily generated and modified.


All CLC bio's workbenches include these features:
  • Detection/localization of restriction sites based on detection parameters such as
    • Minimum recognition sequence length
    • Blunt ends (yes/no)
    • 3' overhang (yes/no)
    • 5' overhang (yes/no)
    • Exclude enzymes with less matches than XX (no. = user input)
    • Possible exclusion of enzymes with more than XX matches (no. = user input)
  • Flexible selection of enzymes:
    • Selection among all enzymes
    • Selection among user-defined enzymes
    • Selection based on specified properties such as overhang, recognition sequence length and/or number of matches.
  • Sorting of listed restriction enzymes
  • Access to all restriction enzymes in REBASE

Output options

These output options are available:
  • Graphical viewing of detected restriction sites as sequence annotations
  • Showing of detected restriction sites in textual format in a table
  • Create new enzyme list from selected enzymes which fulfill match number criteria
Choosing the textual output option will open a new view containing a table with an overview of restriction sites. Choosing the graphical output option will add restriction site annotations to the selected sequence.

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