Artemis: Genome Browser and Annotation Tool

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Links

  • ACT - a DNA sequence comparison viewer
  • DNAPlotter - makes circular and linear interactive plots
  • BamView - interactive display of read alignments in BAM data files

[Genome Research Limited]

New to Artemis?

Example of an Artemis screenshot.

Example of an Artemis screenshot.
Enlarge this image (712 x 827)

The Artemis manual explains how to install and run Artemis and what most parts of the program do. The FAQs may help if you are experiencing problems with Artemis. Also an Artemis poster gives an overview of browsing genomes and visualisation of next generation data in Artemis. There are also use case examples of browsing next generation sequence data.

Full information about the latest release of Artemis can be found in the manual and the current release notes.

License

Artemis is free software and is distributed under the terms of the GNU General Public License. It should run on any system with a recent version of Java.

Citations

The development of Artemis is funded by the Wellcome Trust. If you wish to acknowledge the use of Artemis in a publication, you should cite:

  • Artemis: sequence visualization and annotation.

    Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B

    Bioinformatics (Oxford, England) 2000;16;10;944-5

    PUBMED: 11120685

For Artemis and ACT in database mode:

  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

    Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J and Rajandream MA

    Bioinformatics (Oxford, England) 2008;24;23;2672-6

    PUBMED: 18845581; PMC: 2606163; DOI: 10.1093/bioinformatics/btn529

Using Artemis to visualise read alignments and variation data:

  • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2012;28;4;464-9

    PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703

Development

The development version and source code for the latest release of Artemis is available:

Java Web Start

FTP download

GIT repository

[1] Note for MacOSX: occasionally a browser decides to display the contents of the .dmg.gz archive file rather than downloading it. If this happens hold down the <control> key and click on the download link. A popup menu should appear, containing several choices. One of the choices should be something like "Save Link As" (or perhaps "Download Link...", "Save Link to Desktop", or a variation on this theme). Select that option, and the archive file should be download correctly.

[2] Note for Windows: you may need to shift-click on this link to download the file. Also please ensure that after downloading this file is called "artemis.jar" with no other hidden extensions. Some windows systems change the name so it looks like a zip file, if this happens then do not unzip it just rename it to "artemis.jar".

Downloads

System Requirements

Artemis needs a recent version of Java v1.5 or higher.

For installation instructions please see the Artemis manual.

Download current version

The latest release of Artemis is available for Unix, Macintosh and Windows. It can also be launched with Java Web Start.

Java Web Start

FTP Download

Archive and revisions

[3] Note for MacOSX: occasionally a browser decides to display the contents of the .dmg.gz archive file rather than downloading it. If this happens hold down the <control> key and click on the download link. A popup menu should appear, containing several choices. One of the choices should be something like "Save Link As" (or perhaps "Download Link...", "Save Link to Desktop", or a variation on this theme). Select that option, and the archive file should be download correctly.

[4] Note for Windows: you may need to shift-click on this link to download the file. Also please ensure that after downloading this file is called "artemis.jar" with no other hidden extensions. Some windows systems change the name so it looks like a zip file, if this happens then do not unzip it just rename it to "artemis.jar".

Frequently Asked Questions

Why does Artemis 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 Artemis will use a maximum of 500MB of memory.
You will need to change the art script to fix this problem. Find the line that reads: MEM="-mx500m -ms20m" and change the 500 to a bigger number (try 1000).
To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Artemis.app/Contents. Towards the bottom of the file there are a couple of lines that look like this: 
<key>VMOptions</key>
<string>-Xmx800m</string>
Changing the value after -Xmx will change the memory used by Artemis.
Why does Artemis 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 Artemis can use. The fix is as follows:
Create a shortcut to the Artemis JAR file. Edit the properties of the shortcut and add java -mx250m -jar to the start of the Target: field. -mx250m sets the maximum memory Java will allocate to Artemis. 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 Artemis from then on.

Hints and Tips

Artemis and Hummingbird eXceed
If you use Artemis (or other java programs) with the Hummingbird eXceed X server for Windows you may have problems with borders disappearing. Hummingbird support told David Bauer to go to 
exceed>xconfig>screen definition>set the window manager to "Native"
to force your x applications to use your operating system's window manager.

Chado

Artemis and ACT can be used to connect to Chado databases. They are being developed to read from and write to the database and perform the same functions as the standard Artemis and ACT.

Documentation

Java Web Start

  • Launch Artemis Artemis
  • Launch ACT ACT
  • Launch GeneBuilder GeneBuilder

We welcome contributions to ACT and Artemis and suggestions for new features. An email discussion list is available for this purpose, see the artemis-users information page. Posts to the list since September 2001 are archived at mail-archive.com.

If you have comments about the manual please send them to the ACT/Artemis developers.

* quick link - http://q.sanger.ac.uk/artemis