Category: Tips
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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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MacVectorTip: Working with Oxford Nanopore Long Read Data
Here’s a few tips regarding analyzing long read data from the Oxford Nanopore Technology MinION and GridION machines. First, you should always first create a File | New | Assembly Project and then (typically) click on the Add Reads toolbar button and select the appropriate fastq formatted data files. These are often supplied in compressed…
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Migrating to a serverless concurrent usage license
As well as having a license per user for larger sites we have concurrent usage or network licenses that allow an entire institute, or a large research group to share MacVector. Concurrent usage licenses give you a pool of licenses that can be shared across an entire network. The number of seats defines how many…
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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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Optimizing analysis parameters from the results window
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…
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MacVector 18.7 – View the history of your plasmid
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…
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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…