Zebrafish Genome Resources Workshop

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Zebrafish Genome Resources Workshop

• Mario Caccamo - Sanger Institute
• Judy Sprague - ZFIN
• Lynn Schriml - NCBI

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Workshop
www.sanger.ac.uk/Projects/D_rerio/workshop_Dresden
/
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The Danio rerio sequencing project
www.sanger.ac.uk/Projects/D_rerio
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The Danio rerio sequencing project
whole genome shotgun sequencing
clone mapping and sequencing
WGS reads
BAC ends
integration
assembly release Ensembl
4,519 finished clones (0.69Gb) Vega
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Databases
Vega
Ensembl

• current assembly
• automatic annotation
• BLAST/SSAHA searches
• alignments Uniprot, affy, ESTs
• BAC ends (trace repository)
• Compara database

• finished clones in tiling path
• manual annotation (ZFIN)
• BLAST/SSAHA searches
• alignments/features
• assembly tags

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Vega
finished clones with manual annotation
(collaboration with ZFIN)
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Ensembl
current assembly with automatic annotation
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Compara
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Pre-Ensembl (Zv5)
pre.ensembl.org/Danio_rerio/
Full Ensembl release in preparation
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Assemblies
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Ensemb/Vega new look feel
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Distributed Annotation System (DAS)
genome browser
www.biodas.org
local storage
reference sequence
XML
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DAS features in ContigView
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DAS features in ContigView
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ZF-MODELS
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ZF-MODELS Bioinformatics

• Our role
• Map features in the current assembly (DAS
  servers)
• Data mining tools
• ZF-MODELS database schema

• We have in place DAS servers for
• Enhancer trapping data (Becker lab, Bergen)
• Tilling (Stemple lab, Sanger and Cuppen lab,
  Utrecht)
• Microarray projects (Spaink lab, Leiden, and
  Geisler lab, Tuebingen)

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Acknowledgments
Kerstin Howe Ian Sealy Seth Redmond Tim
Hubbard Zemin Ning Sean Humphray Jane Rogers
Ensembl team Vega team Mapping team High
Performance Assembly team Web team Sequencing
teams