Tag: weeklytip
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MacVectorTip: MacVector 18.8 has a new Preference Reset button.
Very occasionally, you may find MacVector behaving unusually. Perhaps windows are not activating correctly, or functions you have used without issue for many years have suddenly started crashing, taking an excessive amount of time to run or generating nonsensical results. When such issues are reported to MacVector Support, we always try to perform an in-depth…
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MacVectorTip: Use Quicktest Primer to design primers that change encoded amino acids and create restriction enzyme sites
The Quicktest Primer interface is highly interactive and the display shows restriction enzymes and the amino acids sequences of CDS features in the region of interest. Here’s a ~25nt primer aligned against a parental sequence. Restriction enzyme recognition sites are shown in black text. “One-out” sites (e.g. a 5 out of 6 match) are shown with an…
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MacVectorTip: Make Sure You Have Assembler Activated!
In September of 2024, we started including Assembler with all new, upgraded and renewed licenses of MacVector. Assembler is fully integrated within MacVector and is enabled by the license activation code. However, it may be that your lab or institution has a new Assembler activation code after a renewal, but you are still using an…
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MacVectorTip: How to Control the Length of Window Title
If you are having difficulties viewing the name of your sequence in the title bar of a window, it may be because you have “Full Titles” turned on. So if your window title looks like this; Then open MacVector’s Windows menu and deselect Show Full Titles. …and you now just see the name of the…
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MacVectorTip: Assembling Nanopore or PacBio Long-Read Data with Flye
In the previous post we discussed the various ways in which you can analyze Oxford Nanopore’s long read data. For de novo assembly we recommend using Flye, which can also be used with PacBio data. Here are some tips to get the most out of Flye. IMPORTANT: MacVector simply wrappers around the Flye executable algorithm which depends on…
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Handling Gaps in Multiple Sequence Alignment Consensus Calculations
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…
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Automating annotation of sequences via BLAST
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…
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MacVectorTip: Annotating and Comparing Genome Segments
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…
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MacVectorTip: Use Align to Folder to filter NGS data for specific genes
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…
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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…