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

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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Testing pairs of PCR primer

Over the past few releases of MacVector, we have changed primer testing considerably. Now all primer design and testing can be done using Quicktest Primer for a single primer and Primer Design (Primer3) for pairs of primers. If you want to test an existing pair of primers for suitability, use the following steps: Open the […]

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Quickly design a pair of primers to amplify a feature

Designing a pair of primers to amplify a single feature is pretty quick with MacVector. Select a feature in the MAP tab. Run Primer Design/Test(Pairs). Ensure the dropdown menu is set to AMPLIFY FEATURE. Click OK. Check the summary shows that primers have been found and select the spreadsheet and graphical view. Click OK. Tweet

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Clearing the “find” 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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Using the Primer Database to store your lab’s collection of primers

MacVector now directly supports storing primers within a primer database. The Primer Database tool allows you to save and retrieve primers from subsequence files within Primer3 and Quicktest Primer. You can easily create your own primer database, use existing files or import primers from Excel. Many users use subsequence files to store primers, and in […]

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How to quickly design primers to amplify a feature on your sequence

To design a pair of primers to amplify a single feature is pretty quick with MacVector. Select a feature in the MAP tab Run Primer Design (Primer3) Ensure the dropdown menu is set to AMPLIFY FEATURE Click OK Check the summary shows that primers have been found and select the spreadsheet and graphical view Click […]

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101 things you (maybe) didn’t know about MacVector: #37 – Testing PCR Primer Pairs Using Primer3

Over the past few releases of MacVector, we have been adding a lot of functionality to the Quicktest Primer and Primer Design (Primer3) interfaces and slowly removing the old outdated primer design functions. The general strategy is that anything you need to do with a single primer, you can accomplish using the Quicktest Primer interface. […]

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