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Rob Edwards Depts of Computer Science And Biology, San Diego State University

ASM Philadelphia, May 2009. How We Annotated Genomes for Free: Fast and Accurate Functional Analysis Using Subsystems Technology. Rob Edwards Depts of Computer Science And Biology, San Diego State University Mathematics and Computer Sciences Division, Argonne National Laboratory.

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Rob Edwards Depts of Computer Science And Biology, San Diego State University

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  1. ASM Philadelphia, May 2009 How We Annotated Genomes for Free: Fast and Accurate Functional Analysis Using Subsystems Technology Rob Edwards Depts of Computer Science And Biology, San Diego State University Mathematics and Computer Sciences Division, Argonne National Laboratory http://rast.nmpdr.org/?page=Conference

  2. Pigeons If it’s good enough for Google – it’s good enough for me

  3. Annotation Servers • Complete genomes • http://rast.nmpdr.org • Metagenomes • http://metagenomics.theseed.org http://rast.nmpdr.org/?page=Conference

  4. How much has been sequenced? 100 bacterial genomes Environmental sequencing First bacterial genome 1,000 bacterial genomes Number of known sequences Year http://rast.nmpdr.org/?page=Conference

  5. How much will be sequenced? Everybody in USA Everybody at an ASM meeting One genome from every species 100 people Most major microbial environments All cultured Bacteria http://rast.nmpdr.org/?page=Conference

  6. The SEED Family http://rast.nmpdr.org/?page=Conference

  7. Subsystem Spreadsheet

  8. Over 1,000 Subsystems Three level “hierarchy” • Amino Acids and Derivatives • Alanine, serine, and glycine • Serine Biosynthesis • Amino Acids and Derivatives • Lysine, threonine, methionine, and cysteine • Methionine Biosynthesis Make your own subsystems! http://rast.nmpdr.org/?page=Conference

  9. The Annotation Process • Find the phylogenetic neighborhood of your genome • Look for proteins that related organisms have • Core proteins • Subset of all subsystems • Use those calls as a training set for critica/glimmer • Intrinsic training set! http://rast.nmpdr.org/?page=Conference

  10. This one’s for Gary

  11. Automatic Metabolic Reconstruction • Subsystem, GO, and KEGG connections • KEGG EC numbers • KEGG reaction numbers • SEED reaction numbers (Chris Henry) • Metabolic flux models • Automatically generate FBA matrices (Aaron Best/Matt DeJongh; Hope College) http://rast.nmpdr.org/?page=Conference

  12. The Populated Subsystem http://rast.nmpdr.org/?page=Conference

  13. Automatically Compare Metabolic Reconstructions

  14. Find And Suggest Candidate Functions • Rapidly correct missing annotations • Add more members to subsystems • Improves future genome annotations! (especially with new subsystems) http://rast.nmpdr.org/?page=Conference

  15. The Real Live Test • 10 genomes submitted on Thursday at 6 pm • First annotation complete before 8 am Friday • Remaining annotations completed Friday before noon • (there were others in the pipeline too!) http://rast.nmpdr.org/?page=Conference

  16. Subsystems Coverage http://rast.nmpdr.org/?page=Conference

  17. Prophages PHANTOME Mya Breitbart, Matt Sullivan, Jeff Elhai, Rob Edwards NSF Haloferax sulfurifontis prophage

  18. Metagenome Comparisons Metagenomics RAST has 300 public metagenomes Compared using tblastx http://rast.nmpdr.org/?page=Conference

  19. Human Poop

  20. High Salinity SalternsSaN Diego, July 2004 Thanks Beltran Rodriguez-Mueller, Mya Breitbart, & Forest Rohwer

  21. Low salinity salterns High salinity salterns July 2004 Nov 2005

  22. Free workshops on NMPDR, RAST, mg-RAST, SEED Contact Leslie McNeil lkmcneil@ncsa.uiuc.edu or visit http://www.nmpdr.org/ http://rast.nmpdr.org/?page=Conference

  23. Acknowledgements FIG Ross Overbeek Veronika Vonstein Annotators Annotation Servers Rick Stevens Ross Overbeek Folker Meyer Bob Olson Daniel Paarman Mark D'Souza Jared Wilkening Andreas Wilke Environmental Genomics Forest Rohwer Beltran Rodriguez-Mueller Artist Paula Morris http://rast.nmpdr.org/?page=Conference

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