Vbi oomycetes2011 final


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Vbi oomycetes2011 final

  1. 1. MycoCosm & JGI Oomycete Genomics Tools<br />Andrea Aerts<br />Eukaryotic Genomics Program<br />US DOE Joint Genome Institute, Walnut Creek, CA<br /><alaerts@lbl.gov> <br />
  2. 2. US DOE Joint Genome Institute<br />2<br /><ul><li> Opened in 1999
  3. 3. 250+ people
  4. 4. Budget: ~$70M
  5. 5. Location: Walnut Creek, CA</li></ul>www.jgi.doe.gov<br />bioenergy, carbon cycling &biogeochemistry<br />
  6. 6. 3<br />Are you in the right room?<br />IMG<br />MycoCosm<br />70+ annotated eukaryotic genomes<br />genome.jgi-psf.org<br />
  7. 7. 4<br />Outline<br /><ul><li> Eukaryotic Genome Annotation
  8. 8. MycoCosm
  9. 9. Manual Curation</li></li></ul><li>5<br />Started with Human Genome Project<br />
  10. 10. 6<br />Automated Annotation Pipeline<br />Genome assembly and ESTs<br />Repeat Masking<br />Repeat Library<br />Data Mapping<br />External data sets<br />Training predictors<br />Gene Prediction <br />Annotation<br />External gene sets<br />Quality Control<br />Manual curation<br />Optional Inputs <br />Automated Pipeline<br />Staged Portal Release<br />
  11. 11. 7<br />Eukaryotic Gene Prediction<br />Promoter<br />TGA<br />ATG<br />PolyA<br />GT<br />AG<br />Gene model<br />3’UTR<br />5’UTR<br />exons<br />introns<br />mRNA<br />Known genesare mapped onto genomic sequence<br />Known gene<br />Ab initiogene prediction is based on knowledge of general features of gene structure trained on a set of known genes.<br />FGENESH<br />GENEMARK<br />Homology methods build exons around regions of homology and ensure gene structure features.<br />Homolog<br />Predicted model<br />FGENESH+, <br />GENEWISE<br />
  12. 12. 8<br />More Prediction Methods<br />Predicted model<br />Use ESTs/cDNAs to extend, correct or predict gene models<br /><ul><li>ESTEXT</li></ul>ESTs<br />Extended model<br />5’UTR<br />3’UTR<br />Detect orthologs with poor alignments and refine with synteny based methods <br /><ul><li>FGENESH2</li></ul>ATG<br />TGA<br />Genome A<br />Genome B<br />TGA<br />ATG<br />Non-redundant geneset is built from “the best” models from each locus according to homology and ESTs, followed by manual curation<br />Representative set<br />FGENESH<br />GENEWISE<br />EXTERNAL MODELS<br />
  13. 13. 9<br />Outline<br /><ul><li> Eukaryotic Genome Annotation
  14. 14. MycoCosm
  15. 15. Manual Curation</li></li></ul><li>10<br />Ly <br />Comparative View<br />Genome-Centric View<br />www.jgi.doe.gov/fungi<br />
  16. 16. 11<br />11<br />Genome-Centric View<br />Focus:functional genomics, user data deposition and curation<br />
  17. 17. 12<br />New Comparative View<br />
  18. 18. 13<br />Community Building Tools<br />Asilomar, Pacific Grove, CA (Mar 15-20):<br /> Mar 15: Dothideomycetes jamboree<br /> Mar 17: JGI Workshop (Fungi & CSP)<br /> Mar 18: Fungal Tools (MycoCosm)<br />Walnut Creek, CA (Mar 21-24):<br /> Mar 21: Basidiomycetes jamboree<br /> Mar 22: MycoCosm tutorial<br />13<br />
  19. 19. Oomycetes at JGI<br />Phytophthoraramorum<br />Phytophthorasojae<br />improved assembly <br />released “internally” in April 2011<br />Phytophthoracapsici<br />Hybrid Sanger/454 assembly <br />Public release November 2010<br />Phytophthoracinnamomi<br />Currently in sequencing<br />14<br />
  20. 20. 15<br />Outline<br /><ul><li> Eukaryotic Genome Annotation
  21. 21. MycoCosm
  22. 22. Manual Curation</li></li></ul><li>Manual Curation Tools<br />16<br />
  23. 23. Manual Curation Workflow<br />17<br />Find a gene<br />Validate gene structure<br />Choose the best model<br />Fix the structure or report the problems<br />Annotate it!<br />
  24. 24. 1. Find a Gene<br />18<br /><ul><li>Search using keywords
  25. 25. Browse KEGG/GO/KOG lists
  26. 26. Blat/Blast your sequence against genome, transcripts, proteins
  27. 27. Search by ID (Simple search for model name, protein id, gi number)</li></li></ul><li>2. Validate Gene Structure<br />19<br />Using GenomeBrowser, check:<br /> ESTs; Genome conservation; Homology;Other evidence (eg, proteomics, tiling arrays)<br />
  28. 28. 2. Validate Gene Structure, cont<br />20<br />Using Protein Pages, check:<br /> Alignments with homologs; Domains<br />
  29. 29. 2. Validate Gene Structure, cont<br />21<br />Using Cluster Details pages, compare:<br /> sizes and domain composition of orthologs<br />
  30. 30. 4. Fix Gene Structure<br />22<br /><ul><li>If the best not good enough report that it requires editing (AnnotationPage), or fix it (TrackEditor) and then promote it (AnnotationPage)
  31. 31. If there is no model, create it (TrackEditor) and then promote it (AnnotationPage)</li></li></ul><li>5. Annotate Gene<br />23<br />Using AnnotationPage, assign:<br /><ul><li>Gene name/symbol (optional)
  32. 32. Defline (mandatory, will go to GenBank)
  33. 33. Description (optional)
  34. 34. Notes (‘No issues’ if the model is good)
  35. 35. Disposition (‘Catalog’ or ‘Delete’)</li></li></ul><li>Hands-on demo<br />http://genome.jgi-psf.org/Oomycetes/<br />Login<br />oomyceteworkshop@gmail.com<br />workshop234<br />24<br />