High Throughput Computational Sequence Analysis Rob Edwards Argonne National Laboratory San Diego State University.

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Presentation transcript:

High Throughput Computational Sequence Analysis Rob Edwards Argonne National Laboratory San Diego State University

First bacterial genome 100 bacterial genomes 1,000 bacterial genomes Number of known sequences Year How much has been sequenced Environmental sequencing

Everybody in San Diego Everybody in USA All cultured Bacteria 100 people How much will be sequenced One genome from every species Most major microbial environments

High Performance Computing

TeraGrid

The Teragrid National Resource

Life Sciences Gateway to TeraGrid

Subsystems

Subsystems make up metabolism Wikipedia Metabolism

Subsystems are not just metabolism Enzyme complex Cell Machinery Cell Processes

Growth in generation of subsystems

Microbial Genomics Annotation Platform Goal 1: Automate the generation of high quality annotations by leveraging the information contained in SubSystems and FIGfams. Goal 2: Minimize turnaround time. Initial target 48 hours

Automated process consisting of: –Gene calling –Initial annotation of function –Initial metabolic reconstruction Process takes 1-7 hours depending on size and complexity of the genome ~20 genomes per day Password protected, secure, private Release to public databases if required Freely available annotation service

Some estimate of annotation quality

Evaluation / Viewing

Download results We provide a number of export formats: –Genbank, Fasta, GFF3, Excel –can easily be extended to all formats supported by BioPerl Genomes can be deleted by the user at any time (we keep them for max. 120 days) Genomes can be directly imported into the SEED if the user wishes all genomes are password protected

Metagenomics SEED

Metagenome Metabolic Reconstruction

Starch utilization in cow rumens

Metabolic potential in environments

Everybody in San Diego Everybody in USA All cultured Bacteria 100 people Too much will be sequenced One genome from every species Most major microbial environments

Acknowledgements Argonne National Laboratory Rick Stevens Bob Olson Folker Meyer San Diego State University Forest Rohwer Fellowship for Interpretation of Genomes Ross Overbeek Veronika Vonstein The Annotators