It may not be at the cutting edge of sequence analysis but sooner or later most users of such apps are going to have to produce a graphic of their work, whether that is a plasmid map, a tree, an alignment etc..  There’s a world of difference between producing a rough and ready map of a construct for your labbook and producing a publication quality map for a publication. MacVector tries to make producing both as painless as possible. Most of the graphics within MacVector (including the Map view) use the Apple graphics library called Quartz. Quartz uses PDF technology to display graphics (reminiscent of NextStep and DisplayPostscript which was the predecessor to OS X!). It easily allows graphics to be exported directly in PDF format.  More importantly since most modern OS X applications also support PDF format, data can be exchanged via the clipboard using simple copy and paste procedures.  So exporting a plasmid map from MacVector can be as easy as clicking EDIT > COPY in the Map View, moving to the desired application (e.g. Microsoft Powerpoint) and clicking EDIT > PASTE. However, although easy it is important to understand that using copy/paste does not limit the quality in anyway. When you copy and paste from MacVector you are copying as a PDF, rather than the information that is on the screen. PDF is a vector format, as opposed to being a raster format, and can be enlarged to almost any degree without any loss of quality.  Furthermore when you paste into an application that supports this format, such as Adobe Illustrator, then you can directly edit the plasmid map in that applications.

In real terms this means that plasmid maps copied in this way can be resized without any loss of quality and without those jaggy lines.  Fonts will remain crisp as well regardless of what size they are displayed at. Whilst at the booth at the ASM2010 recently we thought it was a great example of how good the graphics could be by showing the metre high plasmid map and other graphics on the booth behind us. These were taken directly from MacVector.  As a smaller example the map below was also copy and pasted directly from MacVector.

Using PDF in this way is the Apple recommended way of dealing with graphics, and it is supported by all the professional applications, such as Adobe Illustrator, Photoshop etc.

In addition the FILE > EXPORT menu will allow you to directly save the MAP view to a PDF file, and if you require a format other than PDF, then you can save a plasmid map in any OS X supported graphics format by utilising PREVIEW. This is an often underlooked utility found in the Applications folder on all Macs. It’s an incredibly useful tool for graphical data as it supports so many formats.

- Open MacVector on the MAP view, and select EDIT > COPY
- Open PREVIEW and select FILE > NEW FROM CLIPBOARD.

Once you’ve done this you can save the file as a PNG, JPG or any supported file.

If you need to obtain a exported image with a specific DPI (e.g. for a paper) then the easiest way is:

- Open MacVector at the MAP view, and select EDIT > COPY
- Open PREVIEW and select FILE > NEW FROM CLIPBOARD.
- Resize the map to the size you require.
- Open FILE – SAVE AS.
- Change the file type to TIFF, and change the DPI to the required value.
- Save the file.

In the next post we’ll discuss how to customise the actual graphics.

Technorati Tags: MacVector, Quartz

Performance

MacVector’s Map View allows the features and results (e.g. restriction enzyme sites) of a sequence to be graphically displayed. So displaying large AND feature rich sequences can result in a fairly slow Map. By large I’m talking about multi megabase sequences where there can be literally tens of thousands of features to show, all with individual labels and individual appearances. That can result in an extremely cluttered appearance. However, being able to visualise a sequence’s features becomes even more important as the size of the sequence increases. You can easily deal with the actual sequence and features of a single plasmid, but try that with a genome!

So to help with larger sequences the following enhancements have been made:

- For restriction enzymes the layout and performance (~20 fold faster!) of cut sites on crowded maps has been improved. Furthermore cut sites are now not displayed if the Map is so crowded that they would not individually resolve. You can view the hidden sites by zooming in to a smaller region or by right-clicking on the display and choosing “Show Results”.

- MacVector now automatically suppresses the display of feature labels for large sequences with many features (controllable from the Map View preferences pane). However, now when you hover the mouse over a feature, a tooltip displays the label of the feature. This is very useful for crowded maps or for when labels are switched off. Features are also now displayed on the inside region of circular maps to prevent features from overlapping each other or the sequence title.

- As well as increased performance the graphics view is now refreshed more optimally to reduce flickering and avoid multiple redraws of complicated layouts, for example when scrolling or resizing a window.

Label customisation

MacVector has always give the user great control in being able to customise the map’s appearance. By default the label of a feature will show the full description qualifier. However, the label can contain whatever you want. Obviously you do not want to waste lots of time changing multiple labels and so MacVector has metatags to define the information that is placed inside the Label. For example using the code below will show the name and location of a feature.

<Description> <Start> 

That’s really useful for restriction enzyme sites.

There are quite a few new metatags for MV 11.1.

<Size> displays the size of a feature in the label.

<Length> (functionally equivalent with the above metatag).

<Total> shows the count of this particular feature type

<Index> shows the order of an individual feature in the above number.

The last two above are also very useful for displaying restriction enzyme cut sites

e.g. <Desc> (<Index>/<Total>) would generate labels like BamHI (1/3)”, “BamHI (2/3) etc.

You can now correctly combine qualifier based metatags. That means <gene>(<number>)” will display My Gene (1) if the qualifiers /gene=”My Gene” and /number=”1” are present in the feature description. Qualifier based meta-tags are skipped if the qualifier doesn’t exist in the feature description (previously the actual meta-tag text e.g. <gene> would have been displayed).

Finally to make all this easier there is a new popup menu in the feature symbol editor that lets you view all of the available meta-tags and insert them into the label. Click on the small triangle to the left of the label edit box.

MacVector 11.1 will be released very shortly.

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MacVector

Here’s the idea – over time you build up a collection of plasmids and sequence fragments of the genes and vectors you work with the most. Perhaps you always like to make your favorite gene appears as a striped red box. Now, when you get a new sequence, just run the auto annotation algorithm (Database | Auto Annotate Sequence) and point it at a folder containing your annotated sequences. The algorithm not only finds the matching features and copies them onto your bare sequence, but it also copies the graphic appearance symbol information. Lets look at an example.

MacVector 11 comes with a large set of pre-annotated vectors. You can find them in the /Applications/MacVector 11/Common Vectors/ folder. We’ve also included an /Annotated Fragments/ folder here with a started set of genes and replication origins you’ll find on many cloning vectors. Here’s a composite graphic image of a selection of those fragments.

There is a plain text copy of pBR322 in /MacVector 11/Tutorial Files/AutoAnnotation/pBR322Ascii.txt. If you open this file in MacVector and toggle its topology to linear, you’ll see there are no features assigned to the plasmid.

The next step is to invoke Database | Auto Annotate Sequence, then click on the Choose… button to select the /MacVector 11/Common Vectors/Annotated Fragments/ folder. Finally, click on the OK button and the algorithm will search through all of the files in the folder looking for matching features. When complete, a report is displayed – when you close that, you’ll see the newly annotated sequence.

In this case, pBR322 has picked up the tetracycline and ampiciliin resistance CDS features, along with the rop gene and replication origin.

Prefer a different way of graphically displaying the features? Try repeating the analysis, but selecting the /MacVector 11/Common Vectors/NEB/ folder – this contains a selection of vectors available from New England Biolabs, formatted to match the appearance in their catalog.

This time, when the algorithm completes, the features take on the typical appearance seen in the catalog. Note that the CDS features have not been duplicated – MacVector realizes the features already exist and just replaces the graphic symbols. You can also optionally set the algorithm to ignore duplicate features completely, in which case the sequence appearance would have been left unchanged.

You can use the Auto Annotation function to scan any folder containing DNA sequences. They don’t have to be in MacVector format, although features from GenBank or EMBL files will be given the default appearance for the feature type. There is a certain amount of fuzziness built into the algorithm – it can handle mismatches and even a few gaps and still identify matching features. We’ll be posting a more detailed tutorial in the next week with more information about the different parameters and limitations of the algorithm. In the meantime, take it for a spin and build up a collection of curated sequences containing all your favorite genes formatted for that great visual impact in your presentations.

The initial change was one of format as the graphics subsystem changed substantially with the release of MacVector 9.5. Instead of using the PICT graphics format, MacVector now uses the Quartz graphic engine that uses PDF for all graphics. This is the standard Apple approved way of displaying any graphics. The advantages behind Quartz are that you can easily generate high quality graphics from MacVector. No longer do you have jagged edges to circular maps, nor fuzzy looking text labels. Furthermore with Quartz you can simply copy, and paste a map into any modern OS X application. For example Microsoft Office 2008 and Adobe Illustrator. You’ll also be able to edit the resulting image in that app too. Apple recommend that all applications use Quartz for graphics, and accept PDF from the clipboard. Microsoft Office 2004 did not accept this, and so we built in a workaround to allow you to still copy high quality graphics into this earlier version of Office.

Additionally in MacVector 10, we introduced the tabbed view, where each tab is simply a different view of the same sequence. We thought it would prove confusing and potentially dangerous for the FILE – SAVE option to have different functions depending on which view is shown. We would hate users to overwrite their valuable sequence with a PDF of a restriction enzyme analysis!

Now the way to save a graphics map is as follows:

To Save a PDF image of a graphic

1. Select the graphics tab and select Edit | Copy.

2. Open the Apple utility ‘Preview.app’ and choose File | New from Clipboard.

3. Select File | Save As.

4. Navigate to the folder where you want to save the graphic data and choose Save.

To Copy a PDF image of a graphic

1. Select the graphics tab and select File | Copy

2. Navigate to the application you want to export the graphic to, and select Edit | Paste in that application.

We did intend to add a separate menu item to perform this directly. However, on the whole users seem to be happy with this approach, and extra menu items sometimes prove distracting.

Incidentally the Map view also allows you to graphically represent your sequence at the base or residue level, if you require.

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MacVector, Quartz