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: 101 Tips

101 things you (maybe) didn’t know about MacVector: #42 – Managing segmented features

If you download eukaryotic genomes from GenBank, you will find that many coding (i.e. CDS) features are segmented and consist of multiple individual segments joined together into a single long feature. You can see an example of this with the human cystic fibrosis transmembrane regulator gene – you find a copy of this in the […]

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101 things you (maybe) didn’t know about MacVector: #41 – Extracting raw data from chromatogram files

Have you ever wanted to know exactly what the total signal value is for individual peaks in a chromatogram file? Perhaps you are looking for mixtures of residues at a particular location and want to get some idea of the relative proportions? You can open .ab1 and .scf chromatogram files directly in MacVector and view […]

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101 things you (maybe) didn’t know about MacVector: #40 – Removing gaps from a DNA or protein sequence

There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig […]

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Restriction enzyme sites and tooltips.

Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab. If you hover your mouse over a restriction site in the Map tab then a tooltip will show you the restriction enzyme recognition site, the location of the cut site, and number of times that enzyme […]

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101 things you (maybe) didn’t know about MacVector: #39 – Viewing sequence residues in the Map view

OK, so this is a very simple tip that many users already know about. But we get enough queries about this functionality that its useful to go over it. The Editor tab has a fair amount of functionality, but it really is designed for editing of sequences at the residue level – we don’t directly […]

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101 things you (maybe) didn’t know about MacVector: #38 – Finding and Opening All The Sequences In Your Collection Containing Specific Genes

How often have you had a vector or sequence open and thought “I’m sure I have other vectors with that gene, but I can’t remember where they are”? If you are using MacVector 13.5, its very easy to quickly search folders on your hard drive to find all the sequences that contain that gene, then […]

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101 things you (maybe) didn’t know about MacVector: #37 – Testing PCR Primer Pairs Using Primer3

Over the past few releases of MacVector, we have been adding a lot of functionality to the Quicktest Primer and Primer Design (Primer3) interfaces and slowly removing the old outdated primer design functions. The general strategy is that anything you need to do with a single primer, you can accomplish using the Quicktest Primer interface. […]

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101 things you (maybe) didn’t know about MacVector: #36 – Changing the circular origin of a plasmid

While most MacVector analysis algorithms can handle circular sequences, its sometimes useful to be able to set the “12 o’clock” point to a different location on the circle. This is easy to do with recent MacVector releases. If you are using MacVector 13.5, then all you have to do is position the flashing caret between […]

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101 things you (maybe) didn’t know about MacVector: #35 – How to make feature arrows in the Map point the other way

We’ve had quite a few users calling up recently to ask how to get the arrows representing a feature in the Map view to point “the other way”. The arrows in the Map view are always shown pointing in the 5′ to 3′ direction relative to the feature, i.e. left to right for a feature […]

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101 things you (maybe) didn’t know about MacVector: #34 – How to fix a -5000 License Activation Error

If you are using an older (pre-13.0) version of MacVector and you try to activate a license on a new computer, or after upgrading your operating system, you may get the following error; This is due to various read/write permissions changes that Apple have made to OS X over the years that prevents MacVector from […]

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