Difference between revisions of "BCS"
From CoGepedia
(Created page with '==WRKY17== Workflow: FeatView->FastaView->CoGeBlast *FeatView: Search for WRKY17 by name: http://genomevolution.org/CoGe/FeatView.pl?accn=WRKY17 *FastaView: Fasta sequence: http:...') |
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==Exploratory analysis== | ==Exploratory analysis== | ||
Workflow: OrganismView->SynMap->explore! | 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 | ||
Latest revision as of 06:52, 24 August 2012
Contents
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
