BCS

WRKY17

Workflow: FeatView->FastaView->CoGeBlast

• FeatView: Search for WRKY17 by name: http://genomevolution.org/CoGe/FeatView.pl?accn=WRKY17
• FastaView: Fasta sequence: http://genomevolution.org/CoGe/FastaView.pl?featid=40606109&gstid=1
• CoGeBlast: http://genomevolution.org/CoGe/CoGeBlast.pl?featid=40606109

Brassica orthologs to AT1G51600

Workflow: FeatView->SynFind->SynMap->GEvo

• FeatView: http://genomevolution.org/CoGe/FeatView.pl?accn=AT1G51600
• SynFind: http://genomevolution.org/CoGe/SynFind.pl?fid=78840469;dsgid=12468
• SynMap (one pair): http://genomevolution.org/CoGe/SynMap.pl?autogo=1;b=6;dsgid1=11022;dsgid2=12468;fid1=78840469;fid2=103070211
  • Smaller, made square, gene coordinates, ordered by chr name: http://genomevolution.org/r/58tx
  • With Ks coloring: http://genomevolution.org/r/58tz
  • Screened for orthologous regions only: http://genomevolution.org/r/58u0
• GEvo: http://genomevolution.org/r/58tt
• Sequences (links to off-site tools for phylogenetics): http://genomevolution.org/CoGe/FastaView.pl?fid=78840469,103070211,102977607,102985284

Collinearity of AT5G38470

Workflow: SynFind->GEvo

• SynFind (searching Arabidopsis thaliana, Arabidopsis lyrata, Brassica rapa):
• GEvo:

Exploratory analysis

Workflow: OrganismView->SynMap->explore!

Expression data support

In development:

• http://genomevolution.org/r/58rk
  • GenomeView with Arabidopsis and 7 test "experiments".
  • High performance experiment data storage engine
  • Different types and density of data

Prototype system:

• http://genomevolution.org/CoGe/GenomeView.pl?z=6&x=20000&dsgid=7043&chr=1
• Real data: 4 methylome data sets
• Does not use the high performance data storage engine

GO Analysis Support

In development:

• Lists of data
  • Genomes
  • Genomic features
  • Experiements

Once completed, can leverage CoGe's annotation system for lists of genes with GO annotations for GO enrichment analysis