Artemis

Overview

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.

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

Download and Installation

Artemis needs a recent version of Java v1.6 or higher.

The latest release of Artemis can be downloaded from our ftp site:

​It can also be launched with Java Web Start:

Launch
Launch with 400 MB

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Launch with 1024 MB

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Launch with 2048 MB

Get Java WebStart

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

For further download and installation instructions, please see the Artemis manual and our GitHub page.

Notes for Download

Note for MacOSX Yosemite (10.10): on the latest version of OSX, ACT mandatorily requires Java v1.6 to run. It will not run with later Java versions.

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.

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 "act.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 "act.jar".

Learn and Support

For more information and advice on using this software please see the Artemis manual and our GitHub page. Also an Artemis poster gives an overview of browsing genomes and visualisation of next generation data in Artemis.

In addition, an email discussion list called artemis-users is available and posts to the list since September 2001 are archived at mail-archive.com

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.

Launching Artemis from the web shows this message: 'Application Blocked by Security Settings'

As of the Java version 7u51 to launch Artemis from these pages the security settings need changing in the Java Control Panel. In the 'Security' tab select the button 'Edit Site List...' and add the following location to the list:

http://www.sanger.ac.uk/resources/software/

For more information see: Java Control PanelWhere is the Java Control Panel on my Mac? Where is the Java Control Panel on Windows?

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.
 

Java Web Start

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Launch Chado Artemis

Launch
Launch Chado ACT

Launch
Launch Chado GeneBuilder

Artemis Course

License and Citation

Artemis is available under GPL3.

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

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

Contact

If you need help or have any queries, please contact us using the details below.

Our normal office hours are 8:30-17:00 (GMT) Monday to Friday.

Publications

  • 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

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

    Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.

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

  • Viewing and annotating sequence data with Artemis.

    Berriman M and Rutherford K

    Briefings in bioinformatics 2003;4;2;124-32

  • Artemis: sequence visualization and annotation.

    Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al.

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

Tool type
Screenshots
  • Artemis edit window

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