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: map view

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. Tweet

Posted in Tips | Also tagged , , , | Leave a comment

Annotating a gene in MacVector

Creating biologically accurate AND beautiful maps of your plasmids is easy in MacVector. All you need to do is select some sequence, then open the FEATURES EDITOR. Every annotation is fully compatible with the Genbank specification and Feature Table. Tweet

Posted in Uncategorized | Also tagged , | Comments closed

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. […]

Posted in Techniques | Also tagged , | Comments closed

Selecting sequence residues in the Map tab

The Map tab is very flexible and allows you to do almost all of the sequence manipulations you might need, without switching tabs. In addition to selecting segments of a sequence by clicking on Restriction Enzyme sites or Features, you can also directly select sequence even when the residues are not visible and represented by […]

Posted in Tips | Also tagged | Comments closed

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 […]

Posted in Techniques, Tips | Also tagged , | Comments closed

Editing the appearance of your sequence maps

Although we think that the default appearance of sequence maps in MacVector is very pretty, sometimes the defaults are not to everybody‚Äôs 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. […]

Posted in Tips | Also tagged , , | Comments closed

The Importance of Topology

MacVector 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 […]

Posted in Tips | Also tagged , | Comments closed

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. […]

Posted in Tips | Also tagged , , | Comments closed

The easiest way to get graphics out of MacVector

You can use MacVector to create beautiful graphical representations of sequences with control over colors, patterns, fonts, symbols and many other aspects of the layout. The easiest way to get the graphics into another application is to simply choose Edit | Copy, switch to the target application and then choose Edit | Paste. The graphics […]

Posted in Tips | Also tagged , | Comments closed

View sequences at the residue level in the Map tab

Many MacVector users do not realize that you can view sequences at the residue level in the Map tab as well as the Editor tab. This has the advantage that you can see restriction enzyme cut sites (including staggered sticky ends) along with the graphical display of features aligned to the residues. You can even […]

Posted in Tips | Also tagged , , | Comments closed