A Wellcome Trust Sanger Institute computer program to study genomes leads the world amongst scientists, a report published today reveals. The program is one of the freely available software tools developed by researchers at the Sanger Institute to accelerate the understanding of genomes.

DNA code is written in four chemical ‘letters’, abbreviated as A, C, T and G and acts as a digital source of information, containing code to make proteins and to control their production. Software to analyse this code is essential to modern biology, both to detect the important regions in the DNA of an organism and to compare the DNA of different organisms.

ACT and Artemis, the paired software tools, allow researchers to find genes and to carry out this comparison on the DNA of any organism. They have been used especially for the study of bacteria and parasites that are some of the world’s major killers such as malaria, TB and typhoid fever, as well as the superbugs MRSA and Cdiff.

The report, by the respected Essential Science Indicators™, produced by ISI Inc., shows that the report describing ACT was one of the ‘Hot Papers’ in the field of Computer Science published in the last two years. Artemis, named for the goddess of the hunt, is a program that allows researchers to view genomes and to find genes in DNA sequence and was also previously a ‘Hot Paper’: ACT, the Artemis Comparison Tool, allows scientists to compare two or more genomes.

“Artemis and ACT were written to meet a need for tools that were portable between systems, easy to install, and simple and intuitive to use. However, they are also very powerful for experienced users, and extremely customisable, making them flexible and usable at both novice and expert levels.”

Professor Julian Parkhill Leader of the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute

The scientific report, published in Bioinformatics on 15 August 2005, describes the ACT program, which is a genome comparison tool. Comparative genomics is of fundamental importance in most modern molecular biology: in the differences between genomes can lie 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, of their evolution and of their acquisition or loss of DNA that alters their pathogenesis and virulence.

“Our freely available software is downloaded extensively. In 2006 there were almost 17,000 downloads of Artemis and 3100 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.”

Dr Tim Carver One of the team that developed ACT

Bioinformatics – the use of computers to handle and interpret the massive amounts of data generated by genome centres such as the Wellcome Trust Sanger Institute – is making a vital contribution to our understanding of the role of genes in health and disease.

More importantly, it is a discipline to which scientists in resource-poor countries can make a significant contribution. The Sanger Institute provides open source software that 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 teach scientists to use the packages, but they also train the trainers for future courses.

“The Wellcome Trust and Sanger Institute hope that these will be sustainable models in which top researchers who are tackling some of the world’s major infectious diseases that have a large impact on human health gain expertise in cutting-edge techniques.”

Professor Julian Parkhill Sanger Institute

Scientists from the Institute’s Pathogen Sequencing Unit returned on Wednesday 20 December from teaching a course at the Kenya Medical Research Institute (KEMRI) in Kilifi, Kenya. The aim is to help train scientists in countries most affected by infectious diseases, who can then pass on their skills: from a course held in Uruguay in June 2006, four South American students will help to teach the course in Uruguay in April 2007.

Through the support of the Wellcome Trust, the Sanger Institute teams are able to make 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.

Professor Parkhill was the ninth-most-cited researcher in Microbiology with an average of 113 citations for each of his publications in the period January 1996 to August 2006.