The paper describes a software tool that is used extensively in academic and commercial laboratories for the comparative analysis of genomic sequences. Comparative genomics is fundamental to modern biology and medical genetics and especially to understanding the behavior of pathogenic and non-pathogenic organisms

“Artemis and ACT are the result of teamwork and have been developed over a number of years in the Pathogen Sequencing Unit (PSU) at the Wellcome Trust Sanger Institute for annotation and visualization of genomes.”

The freely available software has been downloaded extensively: in 2006 (to December) there were 16,500 downloads of Artemis and 3,100 of ACT. These remarkable values demonstrate the demand for the software and show how widely it is used, which feeds through into citations for the paper.

This paper describes an invaluable tool for exploring the similarities and differences between genomes. ACT was specifically designed to be portable between systems, easy to install, and simple and intuitive to use.

However, it is also very powerful for experienced users, and extremely customizable, making it flexible and utilizable at both novice and expert levels.

Comparison between genomes is of fundamental importance in most modern molecular biology: in the differences between genomes can lay the clues to health and disease. Tools that make this comparison easy and intuitive can serve to enable and accelerate work in many areas of biological research. Comparative genomics is especially important in the study of pathogens, their evolution and their acquisition or loss of DNA that alters their pathogenesis and virulence.

Other genomic comparison tools exist. However, they can be overly complex to use and install, and many are proprietary, and part of expensive software packages.

Thanks to our funding by the Wellcome Trust, we are able to make the software freely available for the community to download and use. In addition, the tools themselves are open source, and can be added to or modified by the community.

Artemis and ACT are the result of teamwork and have been developed over a number of years in the Pathogen Sequencing Unit (PSU) at the Wellcome Trust Sanger Institute for annotation and visualization of genomes.

The development has been influenced by the needs of the PSU, which are common to the wider community. In response to the suggestions—and demands—of the wider community, Artemis and ACT have been maintained, improved, and their functionality added to.

Bioinformatics is a discipline to which scientists in resource-poor countries can make a significant contribution. Providing open-source software enables groups from all over the world, especially in developing countries, to access and exploit the large amount of sequence data made available by us and other sequencing groups.

Together with colleagues from the Wellcome Trust, we have developed courses in Artemis, ACT, and other bioinformatics software, which are held in "front-line" countries. Not only do these courses teach scientists to use the packages, but they also train the trainers for future courses. The Wellcome Trust and Sanger Institute are providing a sustainable model of teaching cutting-edge techniques to top researchers who are tackling some of the world’s major infectious diseases with a large impact on human health.

Many of the organisms we work on cause a disproportionate amount of disease in these countries, and we hope that making these tools available can go some way towards supporting scientists in these countries who work on endemic diseases.