Category: Tips

  • Downloading hits from the MacVector 15.5 BLAST Map results tab

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    Chris
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    The MacVector 15.5 BLAST Map results tab is a unique interface for examining the annotations around hits to a query sequence. Each pane in the display represents a High Scoring Segment Pair, as seen in the BLAST Aligned Sequence tab. At the lower left corner of each pane is a Download button – when you…

  • Controlling Automatic ORF Display

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    Chris
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    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…

  • Use the BLAST Map to better identify blast hits

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    Chris
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    With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication…

  • Generating a primer report to send to your Oligo Synthesis service

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    Chris
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    QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more. Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of…

  • How to toggle between 1 and 3 letter amino acid codes

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    Chris
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    MacVector displays amino acid translations in many different result windows. You can drill down to the residue level in the Map tab and see translations of CDS and other translatable features and see translations in the plain text views and the Quicktest Primer interface. The translations can be viewed as either single letter codes or…

  • MacVector’s compatibility with different versions of macOS/OS X

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    Chris
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    We strive to ensure MacVector has good forwards and backwards compatibility. For example, MacVector 15.1 will still open files created with the very first version of MacVector! However, since Apple releases a new operating system every year, and generally make fairly significant “under the hood” changes, it is just not possible to support every version…

  • Clone construction using Digest/Ligate rather than Copy/Paste

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    Chris
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    We’ve previously looked at using Edit | Copy and Edit | Paste to quickly and simply create new constructs using Restriction Enzyme sites. Here’s 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. These work in a very similar…

  • Importing Genbank files from Safari or other web browsers.

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    Chris
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      While MacVector does have a built-in Entrez browser (Database | Internet Entrez Search) you can easily import GenBank formatted text into MacVector via a simple copy and paste approach. Many sequence-oriented web sites have the option of viewing sequences in GenBank format. This format always starts with the text LOCUS and finishes with two…

  • Importing sequences from Addgene into MacVector

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    Chris
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    The Addgene repository is a great place for obtaining expression vectors and other plasmids for your research. Fully annotated sequences are available for most plasmid sequences, although older plasmid deposits may be only partially annotated. All are very easy to import into MacVector. All Addgene sequence deposits have a Genbank formatted sequence. This should contain…

  • Create constructs using MacVector’s Cloning Clipboard

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    Chris
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    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…