Restriction enzyme analysis in MacVector and REBASE

Although there are two different ways to perform restriction enzyme analysis with MacVector, there are also additional places where restriction enzyme sites are shown. All these tools use the same set of restriction enzyme files to recognise enzymes. These files are updated regularly from the REBASE database.

The restriction enzymes are divided into multiple files. There’s the “Common Enzymes” file with commonly used enzymes. That is the default list for all tools. There are also files that are grouped by supplier or all known enzymes. However, if one of these does not suit, it is very easy to create your own set of enzymes. For example all enzymes that are stored in your lab’s freezer drawer!

For each tool you can use the same set of enzymes, or different files for each. So there are multiple ways to select which set of enzymes to use. For all tools you can also choose whether to SHOW ALL ENZYMES or if you have ONLY USE SELECTED ENZYMES checked, then click the OPEN button, ensure that your required sites are selected, and save the file.

  • For dynamically showing restriction enzyme cut sites directly in the Map view, you need to click on MACVECTOR | PREFERENCES | MAP VIEW. Then click the SET ENZYME FILE button and ensure that your file is selected. Please note that since this is calculated dynamically by default it is turned off for sequences larger than 50 kb, although you may increase this limit.
  • For the ANALYZE | RESTRICTION ENZYME…. tool, click the CHOOSE button in the initial dialog and ensure your file is selected. ¬†Again if you are only showing SELECTED ENZYMES click the OPEN button and ensure that these are selected in the file.
  • The QuickTest Primer tool uses the same settings as the Automatic Restriction Enzymes setting in the Map VIEW preferences. However, you also have the option to SHOW ALL ENZYMES or ONLY USE SELECTED ENZYMES.
  • ..and do not forget that all restriction enzyme tools will also optionally show “one out” sites. These are restriction enzymes sites that can be introduced with a single substitution. QuickTest Primer will also show whether these are silent mutations as well. That is whether introducing that site will affect translation.

    Quicktest Primer

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