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Bioinformatics technology developed at Argonne provides new insight into microbial activities
Date:3/14/2008

metagenomics has become increasingly common, scientists have had to address the challenge of analyzing an enormous number of genomic sequences. To ease this process, scientists at Argonne and the Fellowship for Interpretation of Genomes (FIG) developed a system that contains all known DNA and protein sequences. Using this directory, known as SEED, biologists can identify matches between metagenomes and profiles already in the SEED database.

For this study, DNA sequences first were analyzed by using a high-throughput pipeline called the metagenomics RAST (Rapid Annotation using Subsystem Technology) server (http://metagenomics.theseed.org/), developed by researchers from Argonne in collaboration with FIG, the University of Chicago, San Diego State University and Hope College.

Comparing such a huge number of metagenomes is an enormous computational task, said Rick Stevens, a principal investigator in the project and associate laboratory director of Computing, Environment, and Life Science at Argonne. This automated technology revolutionizes the steps needed to acquire an accurately annotated genome.

The sequences then were compared to the SEED platform by using the compute cluster at the National Microbial Pathogen Data Resource. The database allows an overview of the microbial communities and the ability to focus on one metabolic area and detect differences in the proteins being used by the microbes in each environment.

The initial analysis took months of computer time, said Stevens. We eventually determined that more than 1 million sequences from the microbial metagenomes and more than 500,000 from the viral metagenomes were significantly similar to functional genes within the SEED.


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Contact: Steve McGregor
smcgregor@anl.gov
630-252-5580
DOE/Argonne National Laboratory
Source:Eurekalert

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