Daphnia Genome Preview at wFleaBase.org Daphnia Genomics Consortium, Jan. 2006 Don Gilbert, [email protected]

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Transcript Daphnia Genome Preview at wFleaBase.org Daphnia Genomics Consortium, Jan. 2006 Don Gilbert, [email protected]

Daphnia Genome Preview
at wFleaBase.org
Daphnia Genomics Consortium, Jan. 2006
Don Gilbert, [email protected]
D.pulex scaffold_1 Map
D.p. Genome Preview
• D.pulex log50 draft assembly (20050510)
• Annotations
• eukaryote proteomes, gene predictions,
Daphnia EST, microsatellites
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Genome Search : NCBI BLAST
Genome Data Mining : BioMart
Genome Maps : GBrowse
http://wFleaBase.org/prerelease/
Proteome Annotations
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)
BioMart Filter
BioMart Output
BioMart Output
Tables for
Spreadsheets
FastA
GBrowse: Homeobox region
GBrowse: Usage
GBrowse: Usage
GBrowse: Gene Evidence
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
Apollo Gene Annotation
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