Agricultural Microbes Genome 2 Conference Agricultural Microbes Genome 2 Conference
Session: Technology & Bioinformatics
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Two large-scale DOE efforts have matured to the point where they represent significant infrastructure and capabilities that are of potential interest to the Agricultural Microbes community. The Joint Genome Institute located in Walnut Creek, CA is a high-throughput draft-sequencing facility that uses 84 capillary sequencers and runs at a sustained throughput of between 1-2 million lanes/month. The month of October 2000 is the JGI's first microbial month, when 15 microbes of prime interest to DOE's missions will be 6x draft sequenced, with automated analysis and an annotation jamboree to follow within a few months. Clearly, the ability to hold a similar Ag microbial month presents one of the most cost-effective way to rapidly obtain large amounts of high-impact sequence data. The scale of bioinformatics required to work at this volume will be discussed.
The Chemical and Biological Nonproliferation Program (CBNP) is a multi-lab effort to develop and deploy reliable detection methods for toxins and pathogens. Of particular relevance to the Agricultural Microbes community is the bioinformatics infrastructure developed to enable the rapid development of verified DNA signatures for microbial pathogens. Working at the whole-genome level, from Suppressive Subtractive Hybridization (SSH) or raw draft sequence data, we have been able to produce highly-specific signature probe candidates for electronic oligo ordering within 24 hours. We have also used this infrastructure for whole-genome comparisons of pathogens with near-neighbors, for rapid isolation of family-distinct signatures, virulence mechanisms, etc.
The combination of capabilities from these two programs could readily be applied to the needs of the Agricultural Microbes community.