Month: July 2017

  • 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…

  • Confirming a small sequencing project against a reference sequence

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    Chris
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    Align to reference is a perfect tool for mapping small sequencing projects against a reference sequence. It’s perfect for accurately and quickly: – Confirming the sequence of a cloned fragment – Sequencing across the ends of a cloned fragment to confirm the junction sequence – Screening clones from a site-specific mutagenesis experiment to identify successful…

  • 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…

  • Simple but accurate restriction enzyme based clone construction using Copy and Paste

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    Chris
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    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…

  • 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…

  • Tooltips in MacVector: restriction sites, features and reference assemblies

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    Chris
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    Every aspect of MacVector is designed to help you visualise and see information about your sequence and its annotation. Most views have tooltips that display information about restrictions sites, genes, CDS, SNPs, INDELS and much more.