Daphnia Genome Preview at wFleaBase.org

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Presentation transcript:

Daphnia Genome Preview at wFleaBase.org Daphnia Genomics Consortium, Jan. 2006 Don Gilbert, gilbertd@indiana.edu

D.pulex scaffold_1 Map

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/

Proteome Annotations

Annotations Gene Homology Gene Predictions Daphnia Reagent DNA 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

Tables for Spreadsheets FastA BioMart Output

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

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