Tag: primer3
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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.
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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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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. The Tm calculations in MacVector were updated in MacVector 12.6 to use a more modern algorithm. MacVector has always used thermodynamic “nearest neighbor” calculations, but there were two changes…
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Testing primers with MacVector 13
New to MacVector 13 is the ability to quickly test a pair of primers. Previously to test a pair of primers with the Primer3 tool you needed to modify the expected product and reduce the stringency of all parameters so that your primers would be accepted. Now when you enter a pair of primers into…
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Quicktest Primer and restriction sites
With the introduction of the Quicktest Primer tool in MacVector 12.6 primer design became even easier. Being able to slide your primer along a template sequence to see undesirable secondary structure and other attributes in realtime really does make it quicker and straightforward to design good primers. All user feedback we have had say it…