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!

Tag Archives: primer3

Using QuickTest Primer to check for hairpins in sequences, and not just primers.

Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt […]

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Create your own Primer Database.nsub from an Excel spreadsheet

Wouldn’t it be great if there was an easy way of converting that huge primer collection you have into a format that MacVector can use? Well, luckily there is! There is a utility called “Primer Converter” that you can download from our website. To use the utility you first need to get your primers into […]

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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 […]

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Using the Primer Database to store your lab’s collection of primers

MacVector’s Primer Database allows you to save and retrieve primers from a Primer Database with the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites using Primer Database Search. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from […]

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Generating a primer report to send to your Oligo Synthesis service

QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more. Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of […]

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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 […]

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Clearing the history in the Primer and Find dialogs

Many tools in MacVector store a history of sequences, or search terms, that you have previously used. For example, the Find dialog and Primer Design tools. This is accessed using a drop down menu to the right of the box where you would normally type, or paste, your sequence. This is to allow easy access […]

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Calculating the PCR annealing temperature for a pair of primers

MacVector not only calculates the melting temperature (Tm) for any primers you design, but also displays the recommended annealing temperature (Ta) that you should use in PCR experiments using those primers. You can access the main MacVector interface for designing pairs of primers using Analyze | Primer Design (Primer3). From here you can ask MacVector […]

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Using the Primer Database to store your lab’s collection of primers

MacVector 14 saw the introduction of the new Primer Database tool. This allows you to save and retrieve primers from the Primer Database from the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites. The tool comes with a starter database of primers, but you can use existing subsequence […]

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Calculating the melting temperature of PCR primers

Calculating an accurate melting temperature of your oligos, your template and of the predicted product is important to set the cycling parameters of your PCR machine. To test a pair of primers, use Primer Design (Primer3). Open your template sequence Run ANALYZE > PRIMER DESIGN/TEST (Pairs) Click on the Use This Primer checkbox for both […]

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