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!

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 on the plus strand. If you want the arrow to point “backwards”, all you have to do is tell MacVector that the feature is on the minus, or “complementary” strand. This is easy to do and is outlined in the graphic below.

Select the feature that you want to have the arrow point the other way. Click on the Edit button on the toolbar to open the editor for the GenBank representation of the sequence. Now select the Complementary checkbox and click OK. The arrow representing the feature will now point in the opposite direction.

Read more.

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 the residues where you wish the new origin to be and then right-click (or ctrl-click if you don’t have a right mouse button) and select Set Circular Origin from the context-sensitive menu that appears;

If you are using MacVector Free, visit www.macvector.com and download the latest trial to enable this functionality.

If you have an earlier version of MacVector (12.7 or later), you can use the Cloning Clipboard to reset the circular origin. This does require that there is a suitable restriction site at the location where you wish the new origin to be. Open the circular sequence, switch to the Map tab, click on any restriction enzyme site, then click on the Digest toolbar button. That will place the linearized vector onto the Cloning Clipboard. Now click on the Circularize button on the Cloning Clipboard. Then click on the Ligate button in the drop down sheet and a new circular DNA sequence will be created with the selected restriction enzyme site now at the 12 o’clock position. You can learn more about this and view the procedure graphically on our this article.

Over the past few releases of MacVector, we have been adding a lot of functionality to the Quicktest Primer and Primer Design/Test Pairs 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. Any manipulations to handle pairs of primers should be run through the Primer Design/Test Pairs interface.

MacVector 13 made some changes to the Primer Design/Test Pairs interface to allow it to completely substitute for the old Test PCR Primer Pairs algorithm that has now been removed from the Primers sub-menu. It’s pretty simple to test primers using the Primer Design/Test Pairs interface: Open the target sequence, choose Analyze | Primers | Primer Design/Test Pairs and select Use this primer for both the left and right primer. This will let you type/paste sequence data into each of the primer edit boxes and will also change the mode to Test Primer Pair.

When you click on the Test button, MacVector bypasses the normal Primer3 analysis and instead runs an updated variant of the original Test PCR Primer Pair algorithm. The results are presented in a very similar format to the old algorithm, listing the potential problems in red text. The characteristics of the potential product are listed in the Spreadsheet result view, including the recommended annealing temperature to use for the reaction. For more details on using this functionality, please check out this blog post.

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 open them in MacVector. The basic procedure is;

1. Select the gene in your starting vector – this is usually as simple as clicking on the graphical representation of the feature in the Map tab;
2. Select Database | Align To Folder and choose a suitable starting folder – this can be the root of your hard drive, your home folder, a parental folder where you keep all of your sequences or a folder on a remote server;
3. After the job has completed, check the result windows to identify the high quality matches. It’s usually pretty obvious which matches are perfect or close to perfect and which have poor similarity.
4. Select the rows in the Description List corresponding to the matching sequences – you don’t have to select an entire row. As long as you have some part of a row selected, that sequence will be retrieved;



5. Choose Database | Retrieve To Desktop to open those files within MacVector;
6. You can also choose Database | Retrieve To Disk to COPY the files into a new folder on your hard drive. This is a great way to collect all vectors containing a particular sequence in one place, but note that if you make changes to any of the files, the originals will not be modified.

For more details check out this post.