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: Tips

Balancing Velvet KMER and coverage

The Velvet assembly algorithm in MacVector is blazingly fast and generates excellent assemblies. However, you do have to be careful when assembling NGS data to be sure that the parameters you submit are appropriate for the data you are assembling in order to get optimal results. By far the most important parameter is the KMER […]

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Use a right-click in the Editor tab to see if your contig can be circularized

MacVector 16 incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector 16 also includes a new feature to help you with this. If you are assembling […]

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Getting Started with MacVector

Any molecular biologist should be able to start getting useful results within an hour of starting to use MacVector by just exploring the toolbar and menus. Everything is logically named to be obvious. However, there’s still a lot of functionality that a user will never know exists. That is unless you read the manual or […]

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Workflows on designing, testing and storing primers in MacVector

MacVector has many primer tools to make designing, analyzing and cataloging your primers easy. Here are a few typical workflows. Designing primers Amplifying a gene You can design a set of primers to amplify a gene in as little as three mouse clicks. Open your sequence. Open the MAP view, and click on a feature. […]

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MacVector 16 and macOS High Sierra 10.13.4.

Apple have just released macOS® High Sierra 10.13.4. This may appear to be just an incremental update to macOS High Sierra. However, under the hood there are some major changes, not least is a new warning dialog if you are running an older application on macOS High Sierra. With the release of macOS High Sierra 10.13.4 […]

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Assemble bacterial genomes in minutes on your Mac laptop

MacVector with Assembler contains some remarkably powerful algorithms for assembling Next Generation Sequencing (NGS) data. Not so long ago, you needed a powerful Linux server with lots of memory for de novo assembly of whole genomes. But with advances in the efficiency of algorithms and improvements in hardware, it is now possible to assemble quite […]

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Simple Assembly of Sanger Sequencing Files with MacVector Assembler

With MacVector Assembler, assembling ABI Sanger Sequencing files is simple, fast and accurate. MacVector uses the popular phred/phrap/cross_match set of tools from the University of Washington. To improve accuracy, and to help resolve repeats, these tools use “quality scores” (popularly known as “phred scores”), giving them an advantage over many other methods. To assemble two […]

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An overview of assembling sequencing data with MacVector’s Assembler plugin

To assemble various types of sequencing reads, follow these steps. Choose File | New | Assembly Project to create a new empty project file. Then follow one of the following: To create a de novo assembly from Sanger reads Click on the Add Reads tool bar button, then select the sequence files you wish to […]

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MacVector video tutorials on You Tube

There are short video tips on using MacVector on our blog and our YouTube channel. Each one is less than 2 minutes and generally shorter than that! There will be a new screencast every few weeks, so please subscribe to our YouTube channel so you don’t miss any! The latest screencasts include quickly annotating a […]

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Viewing external database entries for features in a sequence.

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 uses, […]

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