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!

Use Analyze->Primer Database Search to scan sequences for primer binding sites

It’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the universal primers bind on either side of the multiple cloning sites. Here I’ve zoomed in the display to make this clearer.

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This is very similar to the Restriction Enzyme search results display, so there are also text tabs containing a list of all the binding sites, along with all the primers that did not bind.

BONUS TIP: If you click on one of the plus strand primers, hold down and click on one of the minus strand primers, then choose Edit | Copy, this will copy the sequence of the predicted PCR product to the Clipboard. Then use File | New From Clipboard to create a new PCR product sequence, complete with all of the features between the two primers.

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