High Throughput Computational Sequence Analysis：高吞吐量计算序列分析.pptVIP

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High Throughput Computational Sequence Analysis：高吞吐量计算序列分析.ppt

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High Throughput Computational Sequence Analysis：高吞吐量计算序列分析

High Throughput ComputationalSequence Analysis Rob Edwards redwards@ Argonne National Laboratory San Diego State University How much has been sequenced High Performance Computing TeraGrid Life Sciences Gateway to TeraGrid Subsystems Subsystems make up metabolism Subsystems are not just metabolism 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 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 Acknowledgements Argonne National Laboratory Rick Stevens Bob Olson Folker Meyer San Diego State University Forest Rohwer red things that are present Four cow samples. * First bacterial genome 100 bacterial genomes 1,000 bacterial genomes Number of known sequences Year 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 The Teragrid National Resource Wikipedia Metabolism /wiki/Portal:Metabolism http://aig.cs.man.ac.uk/gallery/Utopia/ Enzyme complex http://webdeptos.uma.es/ Cell Machinery / Cell Proce