Category Archives: Techniques

Howtos, tips and descriptions of various techniques for using MacVector.

Designing primers for Gibson Assembly with MacVector 17

MacVector 17 has a completely new tool for automated design of ligase-independent cloning strategies. The tool supports 5’ exonuclease driven Gibson assembly as well as the T4 DNA Polymerase 3’ exonuclease “Ligase Independent Cloning” approach. MacVector can automatically design primers when you specify fragments and vectors to use. You can provide custom primers (manually or […]

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Using MacVector’s Agarose Gel tool to design a digest to screen minipreps after a ligation.

How to design a digest to screen minipreps after a ligation. (View full size on website…) Tweet

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RNASeq Expression Analysis with MacVector and Assembler

If you have the Assembler module, MacVector can align millions of NGS reads from RNASeq experiments against large genomes and generate a coverage table displaying the relative expression levels of every gene in a genome. The key to this functionality is that you must have a reference genome with genes annotated as CDS or gene […]

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How to split large fastq files for more manageable assemblies

We’ve previously discussed how important it can be to make sure you are using the appropriate number of fastq reads from an NGS experiment to ensure you obtain the results you are looking for. Using too many reads can confuse algorithms with the massive coverage increasing mis-assemblies due to background errors in the reads. In […]

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Workflows on designing, testing and storing primers in MacVector

MacVector is the best PCR Primer design application on macOS. It has many innovative primer tools to make designing, analyzing and cataloging your primers or oligos easy. Here are a few typical workflows. Designing primers Amplifying a gene You can design a set of primers to amplify a gene in as little as three mouse […]

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Assembling sequencing data with MacVector and Assembler

MacVector has a software plugin called Assembler that integrates directly into the DNA sequence analysis toolkit and provides DNA sequence assembly functionality. Dealing with sequencing reads has never been easier. MacVector includes no less than five different assemblers just a few mouse clicks away from your sequencing reads. Phrap assembles Sanger sequencing reads or existing […]

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Use a right-click in the Contig Editor tab to see if your contig can be circularized

MacVector 16 incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector 16 also includes a new feature to help you with this. If you are assembling […]

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Reference assembly with MacVector and Assembler

MacVector has a plugin module called Assembler that integrates directly into the main package and provides sequence assembly functionality. Assembler was designed from the ground up to be easy to use and allow users to easily manage the large amount of data that sequencing generates nowadays. The Assembler interface is built around the Assembly Project […]

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Use the BLAST Map to better identify blast hits

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 […]

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Confirming a small sequencing project against a reference sequence

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 […]

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