DNAPlotter

DNAPlotter can be used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3.

Citation

DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.

If you make use of this software in your research, please cite as:

DNAPlotter: circular and linear interactive genome visualization.
Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J
Bioinformatics (Oxford, England) 2009;25;1;119-20
PUBMED: 18990721; PMC: 2612626; DOI: 10.1093/bioinformatics/btn578

Software Availability

DNAPlotter is packaged as part of the Artemis Software. The Artemis Software is available under GPL3. The source code can be found on GitHub.

The latest release of Artemis can be downloaded by clicking on the relevant link below:

Or via Bioconda. Simply use:

conda config --add channels bioconda     (to add the bioconda channel)
conda config --add channels conda-forge  (to add the conda-forge channel)
conda install artemis

from the command line, and you’re ready to go (no Java installation required).

For older versions of the software please see the Artemis FTP site

The old v17.0.1 version of the Artemis software required Java version 1.8 to run. All recent releases from v18.0.0 onwards require a minimum of Java 9 and ideally Java 11. This must be installed first. The easiest way to install a non-commercial open source Java version is from AdoptOpenJDK - just select the OpenJDK version and Hotspot options for the relevant platform. See the Artemis user manual for further options. A Java installation is not required for the Bioconda or Docker options.

Installation

For UNIX/Linux

Change directory to the directory you wish to install the Artemis software in. We will use ~/ in this example and in the next chapter.

Uncompress and untar the artemis-unix-release-{version}.tar.gz or artemis-unix-release-{version}.zip file. On UNIX the command is:

tar zxf artemis-unix-release-{version}.tar.gz

This will create a directory called ~/artemis which will contain all the files necessary for running DNAPlotter and the other Artemis tools.

For MacOSX

For MacOSX users, an artemis-macosx-release-{version}.dmg.gz disk image is provided. Double-click on this file in your Downloads folder to unzip it. Then double-click the unzipped artemis-macosx-release-{version}.dmg to mount the “Artemis_Tools” image and display its contents - the Artemis, ACT, BamView and DNAPlotter applications. These apps can then be dragged to any desired location, for example, your dock or desktop. The download file can be unzipped from the command line using gunzip, if necessary:

gunzip artemis-macosx-release-{version}.dmg.gz

There’s also an artemis-macosx-chado-release-{version}.dmg disk image that will start up Artemis with a Chado connection window displayed, if you wish to work connected to a Chado database in Artemis or ACT. This is installed in exactly the same way.

If you wish to run DNAPlotter from the command line instead, then a script is provided within the app package to do this:

Circular-Plot.app/Contents/dnaplotter

For Windows

Copy the artemis-windows-release-{version}.zip file to the directory that you wish to install to and then unzip using an application such as WinZip. This should unpack the artemis.jar, act.jar, bamview.jar and dnaplotter.jar application files.

Usage

Running DNAPlotter on UNIX/Linux Systems

The easiest way to run the program is to run the script called dnaplotter in the Artemis installation directory, like this:

artemis/dnaplotter

Alternatively you can start DNAPlotter with the name of a template file, eg:

artemis/dnaplotter -t templatefile

For other available options use:

artemis/dnaplotter -help

Running DNAPlotter on Macintosh Systems

On MacOSX machines, DNAPlotter can be started by double clicking on the DNAPlotter icon.

You may find that when trying to run the DNAPlotter app for the first time, that you get a security warning window displayed stating that “the application cannot be opened because it is from an unidentified developer” (because the apps are not obtained from the app store). If that’s the case, then just okay the window. Go into your System Preferences via the apple symbol at top left of screen. Then select “Security and Privacy”. You should then see a button called “Open Anyway”, next to some text saying “DNAPlotter was blocked from opening because it is not from an identified developer”. Click on the “Open Anyway” button, which will then display the security warning window again - click the “Open” button on it and DNAPlotter should then start. The application will then open straight away after this, without any further security warnings.

Running DNAPlotter on Windows Systems

DNAPlotter can be started by double clicking on the dnaplotter.jar icon.

Running ACT via Bioconda

The DNAPlotter start script is available in the path, so in a terminal window just use:

dnaplotter

The User Manual

For additional information please see the Artemis manual and our GitHub page. A PDF version of the manual is also available for download here.

Contact

For issues encountered with installing the software please contact your local system administrator. For all other issues, please report them to our Github issues page or email artemis-help@sanger.ac.uk.

FAQ

Why does DNAPlotter run out of memory on UNIX or GNU/Linux even though the machine has lots of memory?

The Java Virtual Machine (JVM) on UNIX has a fixed upper limit on the amount of memory that is available for applications, but this limit can be changed at runtime. As shipped DNAPlotter will use a maximum of 2GB of memory.

There are two ways of fixing this problem:

Change the dnaplotter script. Find the line that reads: FLAGS=”-mx2g -ms100m -noverify” and change the 2g (2 gigabytes) to a bigger number dependent on your machine memory (try 3g), or
Create an ARTEMIS_JVM_FLAGS environment variable set to “-mx2g -ms100m”, adjusting the mx value as required. No script change is required for this, but it would need to be added to your environment.

Why does DNAPlotter run out of memory on MacOSX even though the machine has lots of memory?

To change the memory allocated to DNAPlotter on MacOSX, set the value in the file Info.plist in the directory DNAPlotter.app/Contents. Towards the bottom of the file you will see these lines:

<key>JVMOptions</key>
<array>
<string>-mx2g</string>

Changing the value after -mx will change the max memory used by DNAPlotter. The default is 2Gb.

Why does DNAPlotter run out of memory on Windows even though the machine has lots of memory?

Normally the Java virtual machine artificially limits the amount of memory that DNAPlotter can use. The fix is as follows:

Create a shortcut to the dnaplotter.jar JAR file. Edit the properties of the shortcut and add java -mx2g -jar to the start of the Target: field. -mx2g sets the maximum memory Java will allocate to DNAPlotter (2 gigabytes in this case). We recommend choosing a number that is about 50 megabytes less than the total amount of memory in the machine (to allow for the overhead of windows and the Java virtual machine).

You will need to use the shortcut to run DNAPlotter from then on.

The Artemis Software

The Artemis Software is a set of software tools for genome browsing and annotation