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: pcr

MacVector for Windows: update.

It’s quite a few months since the last update on the development of MacVector for Windows. Work is progressing very well and a lot of the underlying functionality is now finished. The Cloning Clipboard, Restriction Enzyme analysis and QuickTest Primer tools are all done. The release is still some time away, but if you are […]

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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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MacVector Cloning Edition

Does your lab only need a simple DNA analysis application that will help you design primers and cloning experiments? Has your budget been cut to the bone? If the answer is a resounding “yes”, then we’ve released a new version of MacVector just for you. MacVector Cloning Edition provides all of the functionality you need […]

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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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MacVector Talk: January 2015: A review of 2014 and what’s coming in 2015.

MacVector and Assembler: What’s Next! We strive to make MacVector the best sequence analysis app for the Mac. This means our developers are continually at work redesigning every aspect of MacVector, not only to improve functionality, but also to ensure that MacVector is always optimized for the latest versions of OS X. In addition we […]

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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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101 things you (maybe) didn’t know about MacVector: #22 – Aligning Primers To A Reference Sequence

There are a number of different ways that you can find the potential binding locations of primers on a sequence using MacVector. You can use the Quicktest Primer function, or create a Primer database and scan for potential primer binding sites using the Analyze | Nucleic Acid Subsequence analysis algorithm. You can also use the […]

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101 things you (maybe) didn’t know about MacVector: #17 – Creating A Primer Database From An Excel File

Following on from my last post, and Nick’s comment that if you already have a primer collection, its not really practical to re-type them all into MacVector, one-by-one, here’s a useful tip to simplify that process. We have a utility called PrimerConverter.app that you can download from our website. You do need to be using […]

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