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Maize Genome Project

Maize Genome Project. Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA. Maize Genome Project. 3 year sequencing effort Funded November, 2005 Objectives Sequence the maize genespace Genic and regulatory regions Finish 721 contigs: 1 in 100,000 error rate

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Maize Genome Project

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  1. Maize Genome Project • Shiran Pasternak • January 13, 2006 • Gramene SAB Meeting • San Diego, CA

  2. Maize Genome Project • 3 year sequencing effort • Funded November, 2005 • Objectives • Sequence the maize genespace • Genic and regulatory regions • Finish 721 contigs: 1 in 100,000 error rate • Anchor to physical and genetic maps

  3. Project Participants • Arizona Genome Institute (AGI) • Mapping • Washington University at St. Louis (WU) • Sequencing • Cold Spring Harbor Laboratory (CSHL) • Analysis and Annotation

  4. Institutional Layout

  5. CSHL Functions • Annotation • Visualization

  6. Annotation • Internal • Public

  7. Internal Annotation • Prefinishing: Automated • Enrich BAC assemblies with AutoFinish ‘Do Not Finish’ repeat tags • Finishing: Manual • Tag mRNA and ESTs to target problematic regions

  8. Public Annotation • Iteratively redefine gene boundaries • Provide new knowledge on maize genome • Communicate status of the project

  9. Annotation Pipeline • Gramene-Ensembl • Whole genome alignment to rice • ab initio gene prediction with Fgenesh • Evidence-based gene prediction • Repeat analysis • Full annotation on nearly finished BACs

  10. Visualization • Gramene and Ensembl Browser • Existing: Contigs, Genes, Synteny • CMap Views • Whole genome alignment • Sequencing status of BACs & Contigs • Other track suggestions?

  11. ContigView

  12. Synteny View * against Rice

  13. GeneView

  14. New Views

  15. Infrastructure • Hardware • 2 servers, forthcoming node cluster • Dedicated architecture • Genome browser • Database schemata • Annotation pipeline

  16. Data Releases • Ongoing annotation updates (weekly) • Repeats • Gene models • Infrequent genome builds (yearly?) • Orthologs • Syntenic Loci

  17. Impact on Gramene • Cost: $0 • Maize browser will link to Gramene content • Evolving requirements

  18. Staffing Principal Investigators Rick Wilson (WU) Sandra Clifton (WU) Pat Schnable (IA) Srinivas Aluru (IA) Rod Wing (AGI) Rob Martienssen (CSHL) Dick McCombie (CSHL) Doreen Ware (CSHL) Lincoln Stein (CSHL) CSHL Team Shiran Pasternak (Lead) Apurva Narechania (Software) Ben Faga (CMap) Unnamed Data Analyst Unnamed Software Developer

  19. Thanks!

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