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Editing the appearance of your sequence maps
Read more: Editing the appearance of your sequence mapsAlthough we think that the default appearance of sequence maps in MacVector is very pretty, sometimes the defaults are not to everybody’s taste! If you think this way, then changing how maps look is very easy. As usual with MacVector, there are many ways to quickly edit the appearance of a feature or multiple features.…
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The Importance of Topology
Read more: The Importance of TopologyMacVector understands the difference between circular DNA molecules and linear DNA molecules. Not just from the standpoint of how the molecule is displayed on the screen, but also in regard to how the analysis algorithms handle the junction at the ends of the circle. The Topology button controls the underlying linear versus circular state of…
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How to increase the number of graphics levels to stop features overlapping.
Read more: How to increase the number of graphics levels to stop features overlapping.MacVector tries to optimize the Map graphics layout using a trade-off between performance and minimizing unnecessary white space. Sometimes the default settings we have chosen are not ideal, particularly if you are looking at the Map tab of an Align To Reference window where you have a large number of reads overlapping the same region.…
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Displaying CDS features as translations in the Map tab.
Read more: Displaying CDS features as translations in the Map tab.Where appropriate, features can be shown as residues when there is sufficient space to show them (for example when zoomed to residue). By default this is enabled for certain features, e.g. CDS features, genes, but it is controlled from the Symbol Editor and can be turned on/off for most features. In the Map tab, double…
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Calculating the melting temperature of PCR primers
Read more: Calculating the melting temperature of PCR primersCalculating 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. To test a pair of primers, use Primer Design (Primer3). Open your template sequence Run ANALYZE > PRIMER DESIGN/TEST (Pairs) Click on the Use This Primer checkbox for both…
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Removing a restriction site from a plasmid with the Cloning Clipboard
Read more: Removing a restriction site from a plasmid with the Cloning ClipboardBeing 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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The simplest way to export high quality graphics from the Map tab
Read more: The simplest way to export high quality graphics from the Map tabSo you’ve finally go the graphics for that new construct looking absolutely fabulous in MacVector and you want to get it into an image editing program (e.g. Adobe Illustrator, Photoshop or even PowerPoint) ready for that critical presentation. How best to do it? The easiest way, by far, is to simply choose Edit->Copy to copy…
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Keep up to date with MacVector auxiliary files
Read more: Keep up to date with MacVector auxiliary filesMacVector has a large collection of data files that are installed in folders alongside the MacVector application. These include Restriction Enzymes files, Scoring Matrices, documentation, tutorials, a variety of common cloning vectors and even a few useful Applescripts. If you use MacVector’s built-in automatic updater to install each new release and bug-fix, you will find…
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Using BLAST to automatically annotate a sequence
Read more: Using BLAST to automatically annotate a sequenceYou can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST…
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How to select all identical restriction enzyme sites
Read more: How to select all identical restriction enzyme sitesThe 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.…
