Category: Tips

  • MacVectorTip: How to find Restriction Enzymes that only cut outside of a specific region

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    Chris
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    One common cloning related task is to ask MacVector to find restriction enzyme sites that cut in a molecule, but that do not cut in a specific region. e.g. suppose you want to find restriction enzymes that cut pBR322 but that do not cut in the Tetracycline Resistance Gene. To do this, choose the Analyze…

  • MacVectorTip: Simulating mixed plasmid populations in agarose gels

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    Chris
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    We had a recent support call this week from somebody who believed from their agarose gels that they had a mixed population of plasmids from an experiment and wanted to document and determine the banding pattern using MacVector’s agarose gel simulation. You might come across this type of scenario if you have been making site-specific…

  • MacVectorTip: Designing Primers for Gibson Assembly

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    Chris
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    You can use MacVector to design primers for multi-fragment Gibson Assembly, and also generate the predicted recombinant DNA molecule resulting from the assembly. All you have to do to get started is choose the File->New->Gibson/Ligase-independent Assembly… menu item. From there, you can choose the type of assembly (it doesn’t have to be the usual 5’…

  • MacVectorTip: Sign up for an NCBI API key to speed up BLAST results

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    Chris
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    MacVector has a very cool BLAST Map results tab that displays the annotations surrounding any hits from the selected database. Particularly if you are working with prokaryotic sequences, where most BLAST hits these days are to genome sequences. This can really help you see the context of your hits, and let you download just the…

  • MacVectorTip: displaying CRISPR PAM Sites on a sequence

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    Chris
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    CRISPR-Cas9 genetic editing mechanisms require a short (typically 20nt) RNA sequence complementary to a target site next to a Protospacer Adjacent Motif (PAM) sequence. The most commonly used Cas9 nuclease (SpCas9) from Streptococcus pyogenes recognizes the PAM sequence NGG. One new function introduced a few years ago will search for PAM sequences in your sequence.…

  • MacVectorTip: visualizing shared domains in a protein alignment

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    Chris
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    MacVector has a domain-outlining facility for multiple sequence alignments, letting you easily visualize the relationships between features in aligned protein sequences.MacVector’s new multiple alignment file format retains the features/annotations from the sequences that are used to create the alignment. The colors of features from the individual sequence documents are used to outline the domains in…

  • MacVectorTip: correctly flagging PacBio and Oxford Nanopore datasets for assembly by Flye

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    Chris
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    MacVector 17.5 introduced Flye for assembly of PacBio and Oxford Nanopore reads. Flye joins Phrap, Velvet and SPAdes for de novo sequence assembly using along with Bowtie2 and Align To Reference for reference assembly. Flye is an assembler algorithm tuned to assemble low quality long reads such as those produced by the new generation of…

  • MacVectorTip: quality score visualization in sequence assemblies.

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    Chris
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    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. A Shading toolbar button lets you turn on…

  • MacVectorTip: Assembling Fungal Genomes using SPAdes

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    Chris
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    MacVector with Assembler can assemble bacterial genomes in just minutes on quite modest hardware. Currently MacVector has four de novo assembly tools (SPAdes, Velvet, Flye and Phrap). But what of larger genomes? It is currently impractical to run de novo assemblies of Human genomes on a low cost Mac, though RNA-Seq analyses against the human…

  • MacVectorTip: Viewing external database entries for features in a sequence.

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    Chris
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    Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (for example InterProScan). Very useful for when you want to view more detailed or updated information. Within the Genbank specification, which MacVector extensively…