maize genome project shiran pasternak january 13, 2006 gramene sab meeting san diego, ca shiran...
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Maize Genome Project
Maize Genome ProjectShiran PasternakJanuary 13, 2006
Gramene SAB MeetingSan Diego, CA
Shiran PasternakJanuary 13, 2006
Gramene SAB MeetingSan Diego, CA
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•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
Maize Genome Project
Maize Genome Project
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•Arizona Genome Institute (AGI)
• Mapping
•Washington University at St. Louis (WU)
• Sequencing
•Cold Spring Harbor Laboratory (CSHL)
• Analysis and Annotation
Project Participants
Project Participants
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Institutional Layout
Institutional Layout
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•Annotation
•Visualization
CSHL FunctionsCSHL Functions
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AnnotationAnnotation
•Internal
•Public
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•Prefinishing: Automated
• Enrich BAC assemblies with AutoFinish ‘Do Not Finish’ repeat tags
•Finishing: Manual
• Tag mRNA and ESTs to target problematic regions
Internal AnnotationInternal Annotation
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•Iteratively redefine gene boundaries
•Provide new knowledge on maize genome
•Communicate status of the project
Public AnnotationPublic
Annotation
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Annotation Pipeline
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
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•Gramene and Ensembl Browser
• Existing: Contigs, Genes, Synteny
• CMap Views
• Whole genome alignment
• Sequencing status of BACs & Contigs
• Other track suggestions?
VisualizationVisualization
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ContigViewContigView
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Synteny ViewSynteny View
* against Rice
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GeneViewGeneView
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New ViewsNew Views
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InfrastructureInfrastructure
•Hardware
• 2 servers, forthcoming node cluster
•Dedicated architecture
• Genome browser
• Database schemata
• Annotation pipeline
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Data ReleasesData Releases•Ongoing annotation updates (weekly)
• Repeats
• Gene models
•Infrequent genome builds (yearly?)
• Orthologs
• Syntenic Loci
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Impact on Gramene
Impact on Gramene
•Cost: $0
•Maize browser will link to Gramene content
•Evolving requirements
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StaffingStaffing
Principal InvestigatorsRick 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 TeamShiran Pasternak (Lead)
Apurva Narechania (Software)
Ben Faga (CMap)
Unnamed Data Analyst
Unnamed Software Developer
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Thanks!Thanks!