Tag: weeklytip
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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…
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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…
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MacVectorTip: How to Toggle Between Single-Letter and Three-Letter Amino Acid Translation Code
Many views in MacVector display amino acid translations above or below DNA sequences. Typically, these are from CDS features, but can also be the 3/6 frame translation of a sequence. You can display the amino acids as either the single-letter code, or as the three-letter code. You can toggle the setting using the MacVector | Preferences ->…
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MacVectorTip: Drag and drop in the Gibson Assembly window
Over the years, we have added a lot of drag and drop functionality to MacVector. Of course, as with any application, it is not always obvious that you can drag and drop to accomplish tasks because you literally have to drag and drop to discover you can do it at all! So here is the first of…
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MacVectorTip: organizing assemblies and sequencing datasets with the Assembly Project manager.
MacVector’s Assembly Project manager helps you organize multiple sequencing datasets, multiple reference sequences and repeated assemblies. You can store multiple assembly jobs in a single Assembly Project and directly compare multiple runs of the same dataset to determine the best assembly parameters. You can also compare different sequencing datasets assembled against the same reference sequence…
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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 your reference…
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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…
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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…