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  • A few tips on working with digested fragments in the Cloning Clipboard

    The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment. If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligate dialog. However, if you have already selected a pair of enzyme sites, then the…

    Read more: A few tips on working with digested fragments in the Cloning Clipboard
    Jun 1, 2016

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    by

    Chris
    in Techniques, Tips

  • Changing the sequence alignment match and mismatch characters

    Many MacVector analysis functions (e.g. Align To Folder, Create Dotplot and Internet Blast Search) display alignments where there is (by default) a vertical “|” character indicating a match between the query and database sequences. While this is very useful for identifying matching residues, sometimes you might be more interested in those residues that do NOT…

    Read more: Changing the sequence alignment match and mismatch characters
    May 23, 2016

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    by

    Chris
    in Tips

  • Visualizing ORF analysis results in the MAP tab

    The Map tab is a powerful way to visualize and interact with your sequences. You can design primers, ligate and digest fragments from the Cloning Clipboard, visualise translated CDS regions and much more. The Map tab of a Results window is just as flexible as the Map tab of the main sequence window. You can…

    Read more: Visualizing ORF analysis results in the MAP tab
    May 23, 2016

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    by

    Chris
    in Tips

  • Use File -> New From Clipboard to create new sequence documents

    Whenever you have information copied to the clipboard, you can choose File | New From Clipboard and MacVector will interpret any data on the clipboard and create a new document of the appropriate type. While this is most commonly used for DNA and Protein sequence documents, this also works for multiple sequence alignments and data…

    Read more: Use File -> New From Clipboard to create new sequence documents
    May 23, 2016

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    by

    Chris
    in Tips

  • Designing and documenting cloning strategies

    Designing cloning strategies is easy with the Cloning Clipboard. You can perform quite complex ligations by simply dragging compatible ends together. However, when you open this construct a year later, you don’t want to have to look back in your lab book to know how you generated it. Neither do you need to! MacVector fully…

    Read more: Designing and documenting cloning strategies
    May 23, 2016

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    by

    Chris
    in Tips, Tutorials

  • Trial download and updating issues!

    Over the past few weeks we’ve had a few reports of trial downloaders having problems installing the trial. We also had a few calls from users with problems updating to the latest release of MacVector 14.5 (14.5.3). The problem manifests itself by showing an error message that the file is “damaged” and cannot be installed.…

    Read more: Trial download and updating issues!
    May 20, 2016

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    by

    Chris
    in General

  • Calculating the PCR annealing temperature for a pair of primers

    MacVector not only calculates the melting temperature (Tm) for any primers you design, but also displays the recommended annealing temperature (Ta) that you should use in PCR experiments using those primers. You can access the main MacVector interface for designing pairs of primers using Analyze | Primer Design (Primer3). From here you can ask MacVector…

    Read more: Calculating the PCR annealing temperature for a pair of primers
    May 15, 2016

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    by

    Chris
    in Tips

  • Use dot plots to quickly confirm similarity between two sequences

    We occasionally get e-mails from users who think that two sequences should align using ClustalW or the Align To Reference function, but the algorithms cannot find any meaningful matches. In these cases, the first thing I do is open both sequences and then create a dot-plot between them using the Analyze | Create Dotplot |…

    Read more: Use dot plots to quickly confirm similarity between two sequences
    May 15, 2016

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    by

    Chris
    in Tips

  • Downloading BLAST Hits from the NCBI direct to your desktop

    When you use MacVector to run a BLAST search, did you know that you can download any matching sequences directly from the BLAST Description List window? Simply select text on any part of the line(s) representing the sequence you want to download and choose Database | Retrieve To Desktop or Database | Retrieve To Disk…

    Read more: Downloading BLAST Hits from the NCBI direct to your desktop
    May 15, 2016

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    by

    Chris
    in Techniques, Tips

  • Troubleshooting problems with MacVector

    MacVector generally just works. However, it’s a very rare piece of software that does not have occasional technical faults. Every now and again we do get reports to MacVector Support about such technical issues. Whenever we come across such issues we document them and also try to fix it so they never happen again in…

    Read more: Troubleshooting problems with MacVector
    May 15, 2016

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    by

    Chris
    in Tips
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