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: restriction digests

Clone construction using Digest/Ligate rather than Copy/Paste

In previous post we looked at using Edit | Copy and Edit | Paste to quickly and simply create new constructs using Restriction Enzyme sites. This post will look at an alternative approach, using the Digest and Ligate buttons and the Cloning Clipboard. The sequence window Map tab has two buttons called Digest and Ligate. […]

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Simple but accurate restriction enzyme based clone construction using Copy and Paste

The quickest and simplest way to create restriction enzyme generated constructs in MacVector is to use Edit | Copy and Edit | Paste. The strategy to use is identical to copying a paragraph from one Microsoft Word document to insert into a second document. i.e. Select the restriction enzymes flanking the source fragment in either […]

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Restriction enzyme analysis in MacVector and REBASE

Although there are two different ways to perform restriction enzyme analysis with MacVector, there are also additional places where restriction enzyme sites are shown. All these tools use the same set of restriction enzyme files to recognise enzymes. These files are updated regularly from the REBASE database. The restriction enzymes are divided into multiple files. […]

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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 a custom set of restriction enzymes containing just the enzymes in your freezer drawer.

MacVector has multiple tools for displaying restriction enzymes sites in your sequence. All of these tools use Restriction Enzyme files. These are a set of files, updated regularly from the REBASE database, grouped according to reagent supplier. Whereas the default file is “Common Enzymes” if you only purchase enzymes from NEB, then you can choose […]

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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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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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