General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Monthly Archives: May 2016

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 […]

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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 […]

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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 […]

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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 […]

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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. […]

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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 […]

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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 | […]

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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 […]

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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 […]

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Save trace files as images

You can open ABI chromatogram (“Trace”) files directly in MacVector and analyze them like any other sequence. You can also use them in the Align To Reference and Assembler interfaces, where the actual trace data will be displayed, or in any other function that accepts external sequence files. Sometimes you just want to print out, […]

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