Category Archives: Tips

Sequence Assembly: What can Assembler for my lab?

Assembler is fully integrated into MacVector and allows you to manage sequencing data with the familiar MacVector ease. de novo sequence assembly using Phrap, Velvet and SPAdes with Flye for PacBio and Oxford Nanopore. Reference Sequence Assembly: Map millions of reads against genomes, transcriptomes or other reference sequences using Bowtie2. Compare Genomes: Compare two related annotated […]

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Setting the Numbering Origin

Preserving sequence numbering is particularly useful if you want to work on a smaller more manageable region of a large chromosome but wish to retain the original numbering. When you copy a section of a larger sequence and paste the copy into a new MacVector sequence window (or use FILE | NEW FROM CLIPBOARD), the […]

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MacVectorTip: Selecting the sequence from a single restriction enzyme site to the end of a linear sequence

To see the distance between any two points on a sequence is easy. For example select one restriction enzyme site, hold down SHIFT and select the second. The start, stop and length will be shown in the Range Selector (top right corner of every window – see images below). But if you want to see […]

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MacVectorTip: How to Customize the Toolbars of MacVector windows

Like many Mac applications, MacVector takes full advantage of macOS’s ability to add, delete and rearrange the action buttons on window toolbars. To make these changes, right-click (or [ctrl]-click) in the gray space on any toolbar and a context-sensitive menu will appear. Choose Customize Toolbar and a dialog will be displayed with all of the […]

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MacVectorTip: Changing the font used in the Editor, Results and other windows

MacVector is very customizable in how you can produce graphical maps of sequences, assemblies, alignments and more. You can also change the default appearance of MacVector itself. The font used in the Editor and Results window can be changed and increased in size. You are limited to using fixed width fonts (such as Andale Mono […]

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MacVectorTip: macOS Dark Mode and forcing MacVector to open in Light Mode

“Dark Mode makes it easier to stay focused on your work because your content stands out while darkened controls and windows recede into the background” If you use Dark Mode with the Auto setting, then with the short winter days in the northern hemisphere (for our southern hemisphere friends please save this email for six […]

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MacVectorTip: Create custom Codon Usage Tables for ORF analysis and reverse translation

MacVector uses codon usage tables (also called “Codon Bias”) to help you predict protein coding regions in the Analyze | Nucleic Acid Analysis Toolbox functions and also the protein Analyze | Reverse Translation… function. For example, here are the Plus and Minus strand Staden Codon Preference plots aligned under the Plus/Minus ORFs for a Streptomyces […]

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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 […]

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MacVectorTip: Trimming trace files by quality

Many of our users are familiar with the ability of Sequencher to semi-automatically trim poor quality sequences from the ends of Sanger ABI reads. Although it is generally not necessary to do this in MacVector because most of the algorithms can automatically handle poor quality data, there are times when it can be beneficial. So […]

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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 […]

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