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Artemis: a DNA sequence viewer and annotation tool

Summary: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format.

Target: Artemis is targeted toward academic scientists working in the areas of of sequencing/annotating prokaryotic or lower eukaryotic genomes. The software only requires intermediate computer skills, and it will work for anything from a gene to a whole genome.

Introduction

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java >, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL > and GENBANK > database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL >, GENBANK > or GFF > format.

To see Artemis in action go to the examples page >

To get a copy of the most recent stable release of Artemis go to the Release 9 web pages >

Artemis Distribution

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, but is currently best supported on UNIX and GNU/Linux.

System Requirements

Artemis needs a recent version of Java >

• UNIX users should get the latest Java version from the Sun JDK download page >
• GNU/Linux > users should install the Blackdown.org > latest Java release.
• Windows users should get the latest Java version from the Sun download page >
• For MacOSX users should note that it comes complete with a suitable version of version of Java so the UNIX/Linux version of Artemis should work "out of the box".

  Macintosh users with MacOS 8 or MacOS 9 will need to use Artemis 5 release. Releases after this will not support MacOS 8 and 9. Also the Macintosh Runtime for Java (MRJ) > version 2.2 or better should be installed before downloading Artemis.

For installation instructions please see the manual.

Releases

The current stable version of Artemis is release 9 >  The latest user manual is also available online >

Artemis releases:

• Artemis release 9 > - release 9 manual >
• Artemis archive >

Documentation

The user manual > explains how to install and run Artemis and what the most parts of the program do. The HTML files for the manual are also available as a compressed UNIX tar file > or a Zip file >. The manual is also available as one big file> If you have comments about the manual please send them to the Artemis developers > or join the Artemis mailing list >

There is a small list of tips> and frequently asked questions > which may help if you are having common problems.

An on-line demo > of the software is available to guide the user through some of the basic functionality.

The people at the Pseudomonas-Plant Interaction Project have written a tutorial on Artemis >

Mailing list

Contributions to Artemis and bug reports are welcome. 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.co, >

Development

The source code for the latest release of Artemis is available from the Sanger Institute FTP site >

A snapshot of the development version is available here for UNIX > and Windows >

Alternatively if you have Java Web Start > available try clicking below:

Launch Artemis

The Artemis source code is also available from the Sanger Institute web CVS server > in the artemis repository >

cvs -d :pserver:cvsuser(at)cvs.sanger.ac.uk:/cvsroot/pathsoft login cvsuser

cvs -d :pserver:cvsuser(at)cvs.sanger.ac.uk:/cvsroot/pathsoft co artemis

Contact Address

If you have bug reports, questions, comments or suggestions, please contact Artemis developers at artemis(at)sanger.ac.uk. A mailing list > is also available for general discussion.

Acknowledgments

The development of Artemis is funded by the Wellcome Trust's > Beowulf Genomics initiative, through its support of the Pathogen Sequencing Unit >. 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, Barrell B
Bioinformatics. 2000;16;944-5. PMID: 11120685 >

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Annotation of Genomes
Pseudomonas Display
Pseudomonas Act Display
Pseudomonas genomes

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