Tag: restriction digests
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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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MacVectorTip: Restriction enzyme sites and tooltips
Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab. By default MacVector’s Scan DNA For… tool will automatically display restriction enzyme recognition sites in the Map tab. If you hover your mouse over a restriction site, a tooltip will show you the restriction enzyme recognition site, the location of the cut…
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MacVectorTip: Selecting the sequence from a single restriction enzyme site to the end of a linear sequence
To see the distance between any two points on a sequence is easy. For example select one restriction enzyme site, hold down SHIFT and select the second. The start, stop and length will be shown in the Range Selector (top right corner of every window – see images below). But if you want to see…
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MacVectorTip: How to find Restriction Enzymes that only cut outside of a specific region
One common cloning related task is to ask MacVector to find restriction enzyme sites that cut in a molecule, but that do not cut in a specific region. e.g. suppose you want to find restriction enzymes that cut pBR322 but that do not cut in the Tetracycline Resistance Gene. To do this, choose the Analyze…
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MacVectorTip: Simulating mixed plasmid populations in agarose gels
We had a recent support call this week from somebody who believed from their agarose gels that they had a mixed population of plasmids from an experiment and wanted to document and determine the banding pattern using MacVector’s agarose gel simulation. You might come across this type of scenario if you have been making site-specific…
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Using the RE Picker to display restriction enzyme sites in your insert that do not cut your vector.
It’s generally useful with restriction enzyme based cloning to know what restriction enzymes will cut your vector and not cut your insert, or vice versa. There are a few ways to accomplish this with MacVector, but a useful way is to prepare a file of enzymes that do not cut your vector. This is especially…
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Show or hide the RE Picker and the Graphics Palette from the toolbar
MacVector 17’s brand new Restriction Enzyme Picker gives you an interactive way to quickly show what enzymes will digest your sequence. You can dynamically filter what sites are displayed. For example to show just 3’ overhang cutters or use other criteria. What’s more is that you can take a set of cut sites from one…
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How to find one-out Restriction Sites that will change a protein coding sequence
If you are interested in making changes to a protein sequence, it is often useful to make a change to the coding DNA that will create a restriction enzyme site. Conversely, there may be times that you would like to create a site without affecting a protein coding region. You can accomplish this using the…
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Making restriction enzyme cloning easier with MacVector 17’s Restriction Enzyme Picker.
MacVector 17’s brand new Restriction Enzyme Picker is a new floating tool for selecting and filtering Restriction Enzymes to simplify the identification of useful enzyme cut sites. It initially presents you with a list of all available sites in a sequence. However, you can filter on many attributes, such as number of cuts, 5’ or…
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MacVector’s Scan For Missing Features tool makes beautiful plasmid maps easy!
Scan for.. Missing Features: Sequences are automatically scanned and missing features displayed. A simple right-click converts them to a permanent feature. Even blank sequences will be displayed fully annotated with common features. You can even add your own proprietary features.