General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Testing pairs of primers

Quite a few versions back MacVector used to have an old, but well loved, Test PCR Primer Pairs algorithm. Its interface was clunky and it did not take into account modern algorithms for calculating Tm. However, the results were useful. If you liked this tool then you will be pleased to know that the functionality is still in MacVector.

When you enter a pair of primers into Primer Design/Test (pairs) (previously called Design Primers) the interface switches to a new testing mode, TEST PRIMER PAIRS. This tool lets you test pairs of primers using an updated variant of the Test PCR Primer Pairs algorithm.

  • Open ANALYSE > PRIMER DESIGN/TEST (PAIRS)
  • Switch both fields to USE THIS PRIMER and type the primer sequences you want to test into the two edit boxes.
  • The tool switches to TEST PRIMER PAIRS
  • Click on the OK button to run the test.
  • A Summary window will appear showing problems in red text.
  • Select the Test Output, Spreadsheet and Graphical Map checkboxes and click OK.
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