22nd December 2006

A Hot ACT

Genome Program in the Top Three Computer Science Rankings

A Hot ACT

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," said Professor Julian Parkhill, Leader of the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute. "However, they are also very powerful for experienced users, and extremely customisable, making them flexible and usable at both novice and expert levels."

" Artemis and ACT were written to meet a need for powerful and flexible new genome tools that were portable between systems, easy to install, and simple and intuitive to use. "

Prof Julian Parkhill

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," explained Dr Tim Carver, one of the team that developed ACT. "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."

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.

Professor Parkhill explained: "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."

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.

Notes to Editors

Publication details

  • ACT: the Artemis Comparison Tool.

    Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J

    Bioinformatics (Oxford, England) 2005;21;16;3422-3

  • 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

About ISI

ISI Essential Science Indicators from ISI lists highly cited papers in 22 broad fields of science. These papers comprise the top one percent of papers in each field and each year from 1991 through to date. The lists are updated every two months to reflect their current citation counts and also include new papers that enter the top percentile.

The 'Hot Papers' rankings are based on total citations and may change slightly from one bimonthly update to the next as new citations are added to each paper's total.

For full details and citation histories of these papers, see the ISI Essential Science Indicators listings of highly cited papers.

Pathogen Websites

The Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.

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The Wellcome Trust and Its Founder

The Wellcome Trust is the most diverse biomedical research charity in the world, spending about £450 million every year both in the UK and internationally to support and promote research that will improve the health of humans and animals. The Trust was established under the will of Sir Henry Wellcome, and is funded from a private endowment, which is managed with long-term stability and growth in mind.

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Sanger Institute Contact Information:

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