Daphnia Genome Preview at wFleaBase'org

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Daphnia Genome Previewat wFleaBase.org

• Daphnia Genomics Consortium, Jan. 2006

Don Gilbert, gilbertd_at_indiana.edu
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D.pulex scaffold_1 Map
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D.p. Genome Preview

• D.pulex log50 draft assembly (20050510)
• Annotations
• eukaryote proteomes, gene predictions, Daphnia
  EST, microsatellites
• Genome Search NCBI BLAST
• Genome Data Mining BioMart
• Genome Maps GBrowse
• http//wFleaBase.org/prerelease/

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Proteome Annotations
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Annotations

• Gene Homology
• Nine well-annotated proteomes Yeast, Worm,
  Mosquito, Fruitfly, Bee, Zebrafish, Mouse, Human,
  Arabidopsis
• BLAST the Daphnia genome at TeraGrid.org
• Gene Predictions
• SNAP - minimal, fly-gene-model
• Daphnia Reagent DNA
• ESTs, microsatellites,markers
• Collate to Gene Finding Format (GFF)

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BioMart Filter
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BioMart Output
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BioMart Output
Tables for Spreadsheets
FastA
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GBrowse Homeobox region
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GBrowse Usage
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GBrowse Usage
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GBrowse Gene Evidence
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Apollo, Cmap, GMOD Tools

• Improving automated annotation is work
• Jamboree of Experts will do much
• Researchers can contribute annotations
• Apollo editor for Genome Annotation
• View and edit gene models set start, stop
  codons, splicing
• Tools for BLAST, aligning, and sequence checking
• Edits go to Daphnia Chado Database
• Cmap Comparative Maps (genetic, physical, genome)
• More tools developing at www.gmod.org

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Apollo Gene Annotation
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Thanks to these folks

• IU and national TeraGrid group for the CPUs
• JGI and DGC groups for the genome
• GMOD project developers for the tools