Implementation of the Artemis Genome Viewer: Frequently Asked Questions

1. What is Artemis and why should I use it?

Artemis is a free genome viewer and annotation tool developed by the Sanger Institute. Artemis and the Artemis Comparison Tool (ACT) provide a flexible interface where users can:

• upload and view any sequence/annotation file available in Genbank or EMBL format
• search for unannotated sequence motifs
• create new annotations and/or features tailored to the particular interests of the user
• compare genomes of interest

Furthermore, by using Artemis Web Launch and option to enter sequences using their EBI accession number, users can readily view sequences of interest without having to download either the program or the genome sequences

2. How can I use Artemis on the Mac?

Artemis for Windows is easily downloaded and fully functional on OS X. When downloaded onto a Mac, the Artemis program is re-named "Diana". If you are interested in trying the UNIX/Linux version of Artemis, see suggestions for Mac OS X users on the Sanger website Tips and FAQ.

3. Artemis fails to load the large sequence and annotation files

• Some users have found that the latest versions of Artemis recognize EMBL formatted sequence files but not Genbank. To obtain EMBL formatted files go to the Bacterial Genomes page at EMBL, open the plain sequence file and save as text as instructed for Genbank formatted files
  
  
• Alternatively, Artemis may require a greater allocation of memory. To increase the memory allocation, create a shortcut for the Artemis program and right click on the shortcut icon. In the box which specifies the Target you will see the location of the program with which the shortcut is associated. Place quotation marks around the target and infront of the target type: C:\WINDOWS\SYSTEM32\java.exe -jar -Xincgc -Xmx150000000 . If you are using Windows 2000 rather than Windows XP, type: C:\WINNT\SYSTEM32\java.exe -jar -Xincgc -Xmx150000000 .

For example, the text in my targeting box was changed from: C:\Artemis\artemis_v6.jar to:

C:\WINDOWS\SYSTEM32\java.exe -jar -Xincgc -Xmx150000000 "C:\Artemis\artemis_v6.jar"

4. The format of TAB files generated in Artemis looks different from the genbank annotation

Artemis can read entries that are formatted in either EMBL or Genbank formats. However, when creating a new entry within the Artemis program, Artemis will use the EMBL format regardless of how the genome annotation file is formatted. For a description of the differences between the Genbank nad EMBL formats, go to Section 1B of the Artemis Tutorial for PPI Users