By default, MacVector ignores gaps when calculating the consensus of a multiple sequence alignment. However, this can lead to some unexpected results. For example, consider this three sequence alignment where one sequence has a long insertion compared to the other two. In this case it does not seem reasonable to believe that the “consensus” should…
MacVector 18.8 is out and it’s packed with new tools! MacVector 18.8 has tools to help you identify and annotate unknown, unannotated or partially annotated sequences. Ideal for identifying contigs from a de novo assembly. One of these new tools is AutoAnnotate (via BLAST) Auto-Annotate (via BLAST) is similar to Auto-Annotate (local), except instead of using curated sequences on your own…
In last week’s tip we showed you how to filter NGS read data to pull out and assemble just those reads that represent a specific gene of interest. Now let’s see how to annotate the single contig we generated and compare that to a reference genome. First, from the Contig Editor, you can save the consensus in MacVector…
Even the latest Macintosh computers loaded with as much RAM as you can afford will still struggle to de novo assemble genomes much over 50 Mbp. But, often that is not required. If you are just interested in a few genes, or a specific region of a chromosome, you can use Align to Folder to filter the…
The majority of MacVector’s analysis tools use a standard workflow: Optimizing results Once you have run the initial analysis then for subsequent analysis you can just repeat the analysis you have just done and further filter it. To do so you need to rerun the analysis tool except now select the Results window (at the…
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…
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…
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…
MacVector’s Agarose Gel tool can be used to quickly design a restriction digest to screen minipreps following a ligation. Replicate your ligation in MacVector. Create your agarose gel with the correct insert and a vector only lane. Undo the ligation, and repeat with the wrong orientation. Now you will end up with an Agarose Gel…
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…
