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!

Category Archives: Uncategorized

Batch auto annotation of blank sequences with MacVector and AppleScript

Over the past few releases we’ve been making more MacVector tools to be scriptable with AppleScript. The latest is Auto Annotation. Auto Annotation is a great tool for curating your sequences. For example if you receive a unannotated sequence then you can scan it against other sequences to find. Blasting an unknown sequence, fetching the […]

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Using the Primer Database to store your lab’s collection of primers

MacVector’s Primer Database allows you to save and retrieve primers from a Primer Database with the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites using Primer Database Search. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from […]

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Happy Holidays from all of us at MacVector…!

We wish you a happy, healthy and rewarding New Year! Tweet

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Creating a custom set of restriction enzymes containing just the enzymes in your freezer drawer.

MacVector has multiple tools for displaying restriction enzymes sites in your sequence. All of these tools use Restriction Enzyme files. These are a set of files, updated regularly from the REBASE database, grouped according to reagent supplier. Whereas the default file is “Common Enzymes” if you only purchase enzymes from NEB, then you can choose […]

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Controlling the realism of Agarose Gels

The default settings for the agarose gel display in MacVector generate a reasonable photorealistic simulation of an agarose gel. We have actually boosted the intensity of small bands quite significantly, and reduced their diffusion so that smaller bands show up a little more obviously and crisply than they might in real life. Even so, you […]

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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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Annotating the sequence in the Editor tab

You can very quickly annotate a region of interest in your sequence in the Editor tab. For example showing introns in lower case or highlighting CDS features with a colored background. To enter sequences as mixed case. Enable Edit | Transformations | Enable Mixed Case Entry Type your sequence using SHIFT or CAPS LOCK To […]

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Removing a restriction site from a plasmid with the Cloning Clipboard

Being able to remove a restriction site by digesting with an enzyme that cuts at one site to linearize a plasmid, Klenow treating the linear fragment, then religating the fragment, is a useful trick in the lab. It can help you produce a suitable, and simple, cloning site when none previously existed in your vector. […]

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Keep up to date with MacVector auxiliary files

MacVector has a large collection of data files that are installed in folders alongside the MacVector application. These include Restriction Enzymes files, Scoring Matrices, documentation, tutorials, a variety of common cloning vectors and even a few useful Applescripts. If you use MacVector’s built-in automatic updater to install each new release and bug-fix, you will find […]

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Using BLAST to automatically annotate a sequence

You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST […]

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