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!

Some of the most common support calls we get are from users who are not sure how to use a particular feature in MacVector and would appreciate having someone walk through the steps with them. In many of these cases, it turns out that we have published tutorials that have exactly the information they are looking for, but it wasn’t obvious where to find them.

When you install MacVector, it usually gets installed in a folder in the system /Applications/ folder e.g. MacVector 12.6 can be found in the /Applications/MacVector 12.6/ folder. Inside that folder, you will find a folder called /Documentation/. This has electronic versions of the User Guide (MacVector User Guide.pdf) and the Getting Started Guide (GettingStartedGuide.pdf) along with a number of technical “Read Me” files for many of the 3rd party algorithms, plus the following Tutorials;

Align To Reference – Sequence Confirmation Tutorial This shows how you can align one or more sequences (including chromatogram files and next generation sequencing FastQ files) against a reference sequence to confirm the sequence of the reference, look for SNPs in the aligned sequences or screen for successful mutagenesis clones.

Auto Annotation Tutorial This describes the functionality in MacVector that lets you automatically annotate a sequence based on a collection of existing sequences on your hard drive.

Click Cloning Tutorial A tutorial showing how you can create new constructs by simply clicking on restriction enzyme sites, copying fragments and pasting into target vectors.

Gateway+TOPO Tutorial A variant of click cloning using the popular Gateway and TOPO cloning strategies from Invitrogen.

Primer Design Tutorial Check this out to learn about how to use the new interactive Quicktest Primer interface to design primers and find matching primer pairs using Primer3.

Contig Assembly Tutorial A basic tutorial on how to use the add-on Assembler module to assemble sequences from ABI files using the popular phred/phrap/cross_match algorithms from the University of Washington.

NGS Reference Alignment Tutorial How to use the Assembler module to align millions of reads from next generation sequencing runs to genomes using the Bowtie algorithm.

You can also download the tutorials from the Downloads page of our web site.

All of the tutorials use sample sequence files that are found in the /Applications/MacVector 12.6/Tutorial Files/ folder. This folder does NOT contain the actual tutorials, just the sample sequence files – perhaps we need to change that as it does confuse many people.

If you’d like to see tutorials on other subjects, please comment on this blog or send an e-mail to support@macvector.com letting us know.

This is an article in a long running series of tips to help you get the most out of MacVector. If you want to get notified every time a new tip gets published, follow us @MacVector on twitter (or check the feed for the hashtag #101MacVectorTips) or like us on Facebook.

Following on from the graphics tips of the last few posts, here’s one that can save you a lot of time if you are the sort that likes to keep the appearance of your features consistent between sequences (like me). Suppose you have downloaded a sequence from Entrez, or been sent a sequence in GenBank format by a collaborator, and you want to clean it up and make the graphics look nice. Here’s a boring plasmid with the default graphical appearance of a set of gene features;

The first step is to select the feature you want to change – in the image above the AraC gene has been selected, but you can select multiple features so you can change several at one time. Now click on the Copy Feature Appearance button on the Graphics Palette;

The pointer will change to an eye dropper. Position the pointer over the feature whose appearance you want to copy and click the left mouse button. The feature can be in the same window, or, as in the example below, it can be in a different window. There is no need to make that window the active frontmost window – just directly click on the feature;

The selected feature in the original sequence will then update to match the appearance of the feature you clicked on. Every aspect of the source feature’s graphical appearance is copied – the shape, colors, font, position on the map and even any meta tags associated with the label;

This is an article in a long running series of tips to help you get the most out of MacVector. If you want to get notified every time a new tip gets published, follow us @MacVector on twitter (or check the feed for the hashtag #101MacVectorTips) or like us on Facebook.

MacVector’s Map graphics can provide highly detailed views of individual sequences in linear or circular format, or of the results of many analyses. You can print these to a printer with no loss of detail, even if blown up to many magnifications. However, it is often more useful to insert these graphics into other applications such as Microsoft PowerPoint or Adobe Illustrator, or perhaps to save in a suitable format for publishing on a website or a blog.

By far the simplest way to accomplish this is to make sure your graphic is sized appropriately within the MacVector window, then simply choose Edit | Copy. There is no need to make any selection in the window – Edit | Copy will copy the entire graphic to the pasteboard, including any areas that are not currently visible. The data is copied in “PDF” format. This is the popular Portable Document Format more typically associated with document files, but is also used internally by the Mac OS X pasteboard to transfer high quality vector graphics between applications. Once copied from MacVector, you can then directly paste the high quality vector graphics data into most modern graphical applications, including TextEdit, Preview, MS Word, MS PowerPoint, Illustrator, InDesign, Photoshop, Pages, Keynote and many others.

If you would prefer to have the graphical data saved to a file in a particular format (e.g. jpg, png, tif etc) the simplest way is to perform Edit | Copy as described above, then switch to Apple’s Preview.app. This is installed on every Macintosh and can be found in the /Applications/ folder. From Preview, choose File | New From Clipboard and the copied graphics will appear in a new window. Finally, choose File | Save As… and you can choose from most of the common graphics file formats;

This is an article in a long running series of tips to help you get the most out of MacVector. If you want to get notified every time a new tip gets published, follow us @MacVector on twitter (or check the feed for the hashtag #101MacVectorTips) or become our friend on Facebook.

As many US Universities prepare for the upcoming fall semester, now is a good time to remind you that we do offer complimentary teaching licenses for accredited Institutions in all countries. If you are running a practical course involving DNA or Protein analysis for the fall semester (or the autumn term!), you might consider installing MacVector on all the lab computers for the students to use. Contact support@macvector.com and send us the details of the course, the dates the course will run and the approximately enrollment, and we will send you a license you can use on as many machines as you like for the full length of the course.

This is an article in a long running series of tips to help you get the most out of MacVector. If you want to get notified every time a new tip gets published, follow us @MacVector on twitter (or check the feed for the hashtag #101MacVectorTips) or become our friend on Facebook.