The recently released MacVector 18.7 has a new History tab in the Single sequence editor that shows the editing history of your DNA sequences Since the introduction of MacVector’s Cloning Clipboard, all cloning actions (such as ligating a digested fragment into a vector) create a /FRAG feature that records the source of the ligated fragment, the restriction enzymes used to digest it (and […]
Category Archives: Tips
MacVector 18.7: Generating custom Codon Usage Tables (CUT) from your own sequences.
Our latest release, MacVector 18.7, has a new Codon Usage Table viewer. You can use this to generate your own codon usage table (CUT or .bias) files. You can use codon usage tables to optimize codon usage of CDS features for enhanced expression in a different organism. They can also be used in the Nucleic Acid Toolbox to predict protein coding […]
MacVectorTip: Quality scoring of manual edits to your contigs.
Quality scoring of Assemblies and Align to Reference alignments can be visualized directly on the sequence. Residues can be shaded according to their quality scores. These can be displayed anywhere quality values are available, including de novo and reference assemblies in Assembler and Align to Reference alignments. The intensity of the shading of residues indicates […]
How to design a digest to screen minipreps after a ligation.
MacVector’s Agarose Gel tool can be used to quickly design a restriction digest to screen minipreps following a ligation. (View full size on website…) Replicate your ligation in MacVector. Select the two sites, for subcloning your targeted gene, and click DIGEST. Drag the digested fragment from the Cloning Clipboard to your vector click LIGATE. Create […]
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 […]
MacVectorTip: “Nudge” Reads for Better Reference Alignments
The MacVector alignment algorithms are usually pretty good at finding the optimum alignments of reads against a reference sequence. But, very occasionally, they may get confused by repeats or other anomalies in the sequences. Or perhaps you have made after-the-alignment edits: for example, in the Align to Reference Editor, you can insert residues by holding […]
MacVectorTip: Trimming by Quality in sequence assemblies
Many of our users may be 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. […]
MacVectorTip: Use self comparison matrix analysis to identify repeats and inversions
The Dot-Plot analysis (Pustell DNA Matrix) function in MacVector is an extremely powerful way of quickly getting an overview of the similarities between a pair of sequences. However, it can also be used to identify repeats and inversions in a single DNA sequence simply by comparing a sequence to itself. For example here is the […]
MacVectorTip: Restriction enzyme sites and tooltips
Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab. By default MacVector’s Scan DNA For… tool will automatically display restriction enzyme recognition sites in the Map tab. If you hover your mouse over a restriction site, a tooltip will show you the restriction enzyme recognition site, the location of the cut […]
MacVectorTip: Advanced Align to Reference Editing
You can use the Analyze | Align to Reference function to align other sequences (Sanger chromatograms, plain sequences or even NGS data collections) against a reference. Once aligned, the Editor lets you perform all the usual editing functions using an “overwrite” mode – select the residue you want and type the new residue to replace […]