Using pathogen sequence data

Los Alamos National Laboratory is trying to increase the knowledge of specific biological agents that terrorists might use. Researchers are working to develop biological and computational tools to assist in identifying the biological "signatures" that will allow rapid identification of these agents.

The Los Alamos effort provides bioinformatics support to the researchers of the U.S. Department of Energy's Chemical and Biological National Security Program. Los Alamos researchers are studying Yersinia pestis, the bacteria responsible for plague, and Bacillus anthracis, the source of anthrax, and are beginning to study other threat agents. In collaboration with others, this work may lead to better methods of treatment and prevention of major illnesses. In addition, this work is likely to lead to better methods of performing forensic and epidemiological analysis of biological incidents, determining whether an outbreak is natural or engineered and providing a possible identity to perpetrators.

The team also is developing various computational tools to assist in this project. They have developed interactive visualization tools; repeat- analysis tools; and a body of practices and procedures for data exchange that allow researchers to perform analyses more efficiently and exchange data more readily. The project also contributes to the challenge of improving the integration and interoperability of large software systems dealing with large amounts of data.

The bioinformatics work is distinctly a team effort. The members work closely with the best researchers who are investigating the organisms of particular interest to them, regardless of affiliation. The team is working with researchers at Lawrence Livermore National Laboratory on bacterial threat agents, with the U.S. Army Medical Research Institute of Infectious Diseases and the University of Alabama on pox viruses. This work also is coordinated closely with Los Alamos work on sexually transmitted diseases being done for the National Institutes of Health. The NIH work is being done in collaboration with world experts on herpes, papilloma and chlamydia viruses and others.

Said team member Murray Wolinsky of the Lab 's Bioscience Division, "Because of the large need for tools and the limited funds available, we have to avoid 'reinventing the wheel' and use existing tools whenever feasible. For all of these reasons, we stay abreast of the work being done here and elsewhere and focus our efforts on unmet current and future needs."

Such coordination helps ensure that the Lab project uses best practices in sequence annotation and develops tools needed by the community in general.