Category Archives: Techniques

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

MacVectorTip: Grayed out graphics indicate Missing Features

If the graphics in a nucleic acid sequence Map tab appear somewhat “washed out” it is because the graphic items represent common features that MacVector has found that are not annotated on the sequence. For example, here are the Map and Feature tabs of an unannotated cloning vector; You can see a number of features […]

Also posted in Tips | Tagged , | Leave a comment

Simulating DNA electrophoresis in agarose gels using MacVector’s Agarose Gel tool

MacVector has a Agarose Gel interface which allows you to view photo-realistic recreations of restriction digests of linear and circular DNA molecules. The gels look so realistic that users have had a hard time telling photos of their own digests from the simulation in MacVector. When you first use the new tool and compare it […]

Posted in Techniques | Tagged | Comments closed

MacVectorTip: How to find Restriction Enzymes that only cut outside of a specific region

One common cloning related task is to ask MacVector to find restriction enzyme sites that cut in a molecule, but that do not cut in a specific region. e.g. suppose you want to find restriction enzymes that cut pBR322 but that do not cut in the Tetracycline Resistance Gene. To do this, choose the Analyze […]

Also posted in Tips | Tagged , | Comments closed

Designing primers and documenting In-Fusion Cloning with MacVector

The In-Fusion Cloning kits from Takara allow you to perform ligase free cloning of PCR products into vectors in as little as 15 minutes. You can use MacVector’s Gibson Cloning/Ligase Independent tool to design primers for In-Fusion cloning workflows. The In-Fusion kits need a 15nt overlap between the ends of a fragment and the ends […]

Posted in Techniques | Tagged | Comments closed

MacVectorTip: Identifying, Selecting and Assembling NGS reads with a variant genotype

When analyzing/assembling/aligning NGS data, there are many scenarios where you might want to separate out the reads representing different genotypes or variant sequences. MacVector makes this very easy. Take a reference sequence and choose Analyze->Align to Reference. Now click the Add Seqs button and select and add your NGS data files. NOTE: if your reference […]

Posted in Techniques | Tagged , | Comments closed

MacVectorTip: Filtering NGS Data to retrieve reads matching a known sequence

So you just got your NGS reads back from that sequencing experiment and, wow, what a HUGE amount of data. Wouldn’t it be easier to handle if you could pare that down to just the gene/plasmid/sequence(s) you are interested in? MacVector to the rescue as it can read and filter fast/q files, even if they […]

Posted in Techniques | Tagged , | Comments closed

MacVectorTip: Use Bowtie to remove contaminating reads prior to NGS Assembly

MacVector with Assembler can use Velvet and/or SPAdes for fast and memory efficient de novo NGS assembly of modest sized genomes (typically up to 40 Mbp or so) even on a laptop. One common task is to assemble NGS data from BAC clones.However, one problem that often arises is that the BAC DNA preparations may […]

Posted in Techniques | Tagged , , | Comments closed

Applescript: batch translation of CDS features

Apple’s AppleScript (along with Javascript for Automation) is an easy to write and easy to understand language that allows you to easily automate tasks in supported applications. Many Apple applications have a AppleScript Dictionary that defines what functions you can automate. MacVector has many such functions in its AppleScript Dictionary. You can auto annotate multiple […]

Also posted in Tips | Tagged , , | Comments closed

MacVectorTip: Viewing genotype changes in Align to Reference assemblies

The latest releases of MacVector, MacVector 18.0.1 (Intel) and MacVector 18.1.1 (Intel and Apple Silicon) have some tweaks to the output of the SNPs tab in the Align to Reference assembly window. The genotypes of any SNP changes now follow a consistent standard, and short deletions are also reported. If the region containing the nucleotide […]

Also posted in Releases, Tips | Tagged , , , , | Comments closed

CRISPR tools in MacVector 18

If you are using CRISPR editing techniques then there are two useful functions in MacVector for you: Finding CRISPR Cas9 PAM sites. You can also use Scan DNA FOR.. tool to automatically show sites on all sequences. Screening sequences for CRISPR introduced INDELS

Also posted in Releases, Tips | Tagged | Comments closed