Author: Chris
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Controlling The Automatic ORF Display in MacVector 15.5
MacVector 15.5 automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. The setting for this are controlled by the MacVector | Preferences -> DNA Map pane, along with the automatic Show restriction sites settings. The Minimum Number of Codons setting is fairly obvious. 5’ ends are…
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MacVector 15.5 is out: Graphical BLAST and automatic ORF display.
Our latest release, MacVector 15.5, introduces an entirely new way to view the results of BLAST searches, with an interactive graphical interface that let’s you easily visualize where your query maps to a hit. Unannotated Open Reading Frames are now automatically displayed whenever you open a DNA sequence. A number of changes to the Align…
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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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How to change the default appearance of features
If you download a sequence from Entrez, or open a sequence that is not in MacVector format, MacVector assigns a default appearance to any features on the sequence. For example, CDS features are shown as a blue arrow with a Helvetica 9 point font label. With the advent of ultra high resolution displays, you may…
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Use File->Export in the Contig Editor to save selected reads
Last week we covered the fact that you can use File->Export to save sequences or alignments in different formats. Delving down deeper into this, some of the views will save different types of data based on what you select in the format menu. The best example of this is the Contig Editor. If you choose…
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Use File->Export to save sequences in a different file format
Over the years, Apple have changed the recommended layout and functionality of the File menu. At MacVector, we always try to follow Apple’s guidelines wherever possible so that new users will feel comfortable with familiar menus. However, long-term users may experience some confusion, particularly if you want to save sequences in a different format. Here…
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How to reset the graphics palette if it disappears
The floating graphics palette is extremely useful for helping to configure the display of the Map tab. You can easily toggle the visibility of any individual or group of features and adjust many aspects of the display. MacVector does try to remember the last position you moved this to so its there ready for you…
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Tips for finding ORFs in your sequence
We’ve talked in previous tips about annotating open reading frames as CDS features. However, what if your sequence has no annotated ORF? MacVector’s ANALYZE | OPEN READING FRAMES… tool will help you find any quickly. However, if you are new to this tool there are a few options that may prove initially confusing. These options…
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Using QuickTest Primer to check for hairpins in sequences, and not just primers.
Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt…