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: cloning

How to change the default appearance of RE sites

MacVector is extremely customizable. If you don’t like the defaults we supply, its very easy to change them. Lets look at restriction enzyme sites. By default we show unique sites in small red letters and sites that cut more than once in small blue letters. But suppose you want something bigger, bolder and, well, more […]

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Working with digested fragments in the Cloning Clipboard

The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment. – If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligation dialog. However, if you have already selected a pair of enzyme sites, then […]

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Creating cloning construction flowcharts in third party applications

We’ve previously discussed how every ligation is documented. You get a Frag annotation that contains the date, source sequence, enzymes used and any end modification that was done to that fragment during the ligation. However, we had regular requests to make it easier for users to document their constructs in other ways. For example, being […]

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Controlling the realism of Agarose Gels

The default settings for the agarose gel display in MacVector generate a reasonable photorealistic simulation of an agarose gel. We have actually boosted the intensity of small bands quite significantly, and reduced their diffusion so that smaller bands show up a little more obviously and crisply than they might in real life. Even so, you […]

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A few tips on working with digested fragments in the Cloning Clipboard

The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment. If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligate dialog. However, if you have already selected a pair of enzyme sites, then the […]

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Designing and documenting cloning strategies

Designing cloning strategies is easy with the Cloning Clipboard. You can perform quite complex ligations by simply dragging compatible ends together. However, when you open this construct a year later, you don’t want to have to look back in your lab book to know how you generated it. Neither do you need to! MacVector fully […]

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Create constructs using the Cloning Clipboard

You can create new constructs in MacVector by selecting two restriction enzyme sites, choosing Edit -> Copy, selecting a target restriction site in a different molecule and then choosing Edit -> Paste. It works great and fully understands compatible overhanging sticky ends preventing you from accidentally creating biologically impossible molecules. However, a far more flexible […]

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Removing a restriction site from a plasmid with the Cloning Clipboard

Being able to remove a restriction site by digesting with an enzyme that cuts at one site to linearize a plasmid, Klenow treating the linear fragment, then religating the fragment, is a useful trick in the lab. It can help you produce a suitable, and simple, cloning site when none previously existed in your vector. […]

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How to select all identical restriction enzyme sites

The Automatic Restriction Enzyme Analysis tool that is displayed on the sequence in the Map tab is very powerful. It automatically displays a custom set of restriction enzyme recognition sites on every sequence that you open. Unique recognition sites are displayed in red and sites with two or more cut locations are displayed in blue. […]

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Restriction enzyme sites in cloning vectors show compatible ends with fragments in the Cloning Clipboard

If you are looking for compatible cloning sites for a fragment, MacVector has a simple color-coded function to identify potential target sites in a vector. First select the fragment you wish to clone by clicking on two enzymes in the Map view of a single sequence document or from a restriction enzyme search result. Then […]

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