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Vbi oomycetes2011 final

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JGI tutorial

JGI tutorial

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