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Vbi oomycetes2011 final
 

Vbi oomycetes2011 final

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JGI tutorial

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    Vbi oomycetes2011 final Vbi oomycetes2011 final Presentation Transcript

    • MycoCosm & JGI Oomycete Genomics Tools
      Andrea Aerts
      Eukaryotic Genomics Program
      US DOE Joint Genome Institute, Walnut Creek, CA
      <alaerts@lbl.gov>
    • US DOE Joint Genome Institute
      2
      • Opened in 1999
      • 250+ people
      • Budget: ~$70M
      • Location: Walnut Creek, CA
      www.jgi.doe.gov
      bioenergy, carbon cycling &biogeochemistry
    • 3
      Are you in the right room?
      IMG
      MycoCosm
      70+ annotated eukaryotic genomes
      genome.jgi-psf.org
    • 4
      Outline
      • Eukaryotic Genome Annotation
      • MycoCosm
      • Manual Curation
    • 5
      Started with Human Genome Project
    • 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
    • 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
    • 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
    • 9
      Outline
      • Eukaryotic Genome Annotation
      • MycoCosm
      • Manual Curation
    • 10
      Ly
      Comparative View
      Genome-Centric View
      www.jgi.doe.gov/fungi
    • 11
      11
      Genome-Centric View
      Focus:functional genomics, user data deposition and curation
    • 12
      New Comparative View
    • 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
    • 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
    • 15
      Outline
      • Eukaryotic Genome Annotation
      • MycoCosm
      • Manual Curation
    • Manual Curation Tools
      16
    • Manual Curation Workflow
      17
      Find a gene
      Validate gene structure
      Choose the best model
      Fix the structure or report the problems
      Annotate it!
    • 1. Find a Gene
      18
      • Search using keywords
      • Browse KEGG/GO/KOG lists
      • Blat/Blast your sequence against genome, transcripts, proteins
      • 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)
    • 2. Validate Gene Structure, cont
      20
      Using Protein Pages, check:
      Alignments with homologs; Domains
    • 2. Validate Gene Structure, cont
      21
      Using Cluster Details pages, compare:
      sizes and domain composition of orthologs
    • 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)
      • If there is no model, create it (TrackEditor) and then promote it (AnnotationPage)
    • 5. Annotate Gene
      23
      Using AnnotationPage, assign:
      • Gene name/symbol (optional)
      • Defline (mandatory, will go to GenBank)
      • Description (optional)
      • Notes (‘No issues’ if the model is good)
      • Disposition (‘Catalog’ or ‘Delete’)
    • Hands-on demo
      http://genome.jgi-psf.org/Oomycetes/
      Login
      oomyceteworkshop@gmail.com
      workshop234
      24