Tag: primer3
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Optimizing analysis parameters from the results window
The majority of MacVector’s analysis tools use a standard workflow: Optimizing results Once you have run the initial analysis then for subsequent analysis you can just repeat the analysis you have just done and further filter it. To do so you need to rerun the analysis tool except now select the Results window (at the…
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MacVector’s Primer Database – Importing primers from Excel
Many molecular biologists keep lists of their primer sequences in Excel or some other spreadsheet tool. Previously MacVector had a separate utility that allows you to import primers kept in spreadsheet format into a Primer Database for direct use within MacVector. With the release of MacVector 18.2 we have integrated this functionality within MacVector. Rather…
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Working From Home: An overview of primer design workflows in MacVector.
Working from home?. We want to help familiarize you with the wide range of functionality in MacVector that you may never have used before. Here’s an overview of workflows for designing, testing, documenting and storing primers. You may not have a PCR machine on the kitchen table, but why not take the time to store…
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Primer validation with MacVector: Primer3, Covid19 and primer design
The CDC recently published diagnostic real-time primers for identification of SARS-CoV–2 in any person suspected of having COVID–19. Unfortunately as pointed out on the Biome Informatics blog these primers have issues that should have easily been detected had the primers been tested using a good quality primer testing tool (the linked blog post uses Primer3).…
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Calculating the optimal PCR annealing temperature
MacVector has several tools to help with primer design and testing. The Analyze | Primer Design/Test (Pairs) function uses the popular Primer3 algorithm to find suitable pairs of primers to amplify specified segments of DNA. You can also enter pairs of pre-designed primers and test their suitability for use in PCR. In both cases, the…
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Scan For… Missing Primers: Automatic Primer Binding Site Display
One new feature in our MacVector 17 release is the ability to automatically display primer binding sites in each DNA sequence that you open. Here’s an example of a couple of primers displayed on the popular pET 47b LIC cloning vector on each side of the LIC cloning site. The image shows how MacVector 17…
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Workflows on designing, testing and storing primers in MacVector
MacVector is the best PCR Primer design application on macOS. It has many innovative primer tools to make designing, analyzing and cataloging your primers or oligos easy. Here are a few typical workflows. Designing primers Amplifying a gene You can design a set of primers to amplify a gene in as little as three mouse…
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Adding a primer to MacVector’s Primer Database.
MacVector’s Primer Database tool makes it easy to store your lab’s regular primers. It 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 Primer Database will also store tails and allow you to specify…
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Annotating primers to your sequence with MacVector
Designing a pair of primers to amplify a single feature is pretty quick with MacVector. Once you have designed a pair of primers with MacVector, you can quickly annotate both the primers and product to your sequence template. The annotation contains a timestamp and the primer’s characteristics. It also contains the full sequence of the primer,…
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Testing pairs of primers with MacVector
MacVector’s Primer Design tools makes it easy to test your primers. You can insert them directly from MacVector’s Primer Database or copy and paste them.