Category Archives: Techniques

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

Primer validation with MacVector: Primer3, Covid19 and primer design

The CDC recently published diagnostic real-time primers for identification of SARS-CoV–2 in any person suspected of having COVID–19. Unfortunately as pointed out on the Biome Informatics blog these primers have issues that should have easily been detected had the primers been tested using a good quality primer testing tool (the linked blog post uses Primer3). […]

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How to copy a specific short amino acid translation of a sequence

There can be times when you are messing about with open reading frames, inserting residues to change frames to try to get the perfect CDS fusion. The MacVector single sequence Editor will show those (click and hold on the “Display” toolbar button) but if you select and copy, only the DNA sequence (with any overlapping […]

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Use Database | Auto-Annotate Sequence to annotate prokaryotic genomes

The continuing advances in Next Generation Sequencing have made it relatively low cost to sequence prokaryotic genomes. Many scientists are embarking on large projects to sequence multiple related genomes. These might be clinical isolates of the same species exhibiting different pathogenetic properties, environmental isolates from different sites, or a study over time of the changes […]

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Identifying transposon insertion sites from multiplexed NGS data

Transposon mutagenesis is a common approach for investigating gene function in bacterial genomes by selecting for clones where the transposon inserting into the genome has generated a specific phenotype. You can then simply sequence the entire genome of each clone by NGS to identify the transposon insertion site. To lower the cost of such experiments, […]

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Human Transcriptome RNA-Seq Analysis Using MacVector

With MacVector Pro and Assembler you can use Bowtie to perform RNA-Seq analyses using NGS data. The interface even has specialized output tabs listing the coverage information and statistics for each annotated CDS and gene feature on the genome. You can download a short tutorial and a sample dataset that illustrate the analysis workflow using […]

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

MacVector 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 also includes a tool to help you with this. If you are assembling reads representing plasmid […]

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Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features

There are many genomes in the Genbank database that cannot be downloaded as single annotated sequences. These might be large multi-chromosome eukaryotic genomes, but, increasingly, partially sequenced bacterial chromosomes where the major contigs have been annotated using the NCBI annotation pipeline. Typically, when you encounter these, there are options to download annotated versions of these […]

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Optimizing Align To Folder Parameters for use with NGS Data

You can use the Database | Align To Folder function to scan large fasta or fastq files containing NGS data to find and retrieve just those reads that match a specific target sequence. The search is aware of paired-end reads, so when you retrieve hits, both reads of a pair will be saved into a […]

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Comparing multiple reference assemblies with MacVector 17

MacVector 17 has a greatly improved Assembly Projects manager, for better organization of multiple sequencing datasets, multiple references sequences and repeated jobs. Every time you run a new assembly job (either a reference assembly or de novo). A new job object is created in the Assembly Project window contains resulting contigs and any unaligned reads […]

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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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