CoGe Plant Bioinformatics Workshop

Presentation:

• (45M) Mac Keynote: http://data.iplantcollaborative.org/quickshare/2edd7ae768fb6c0f/2012_JCVI-CoGe-Workshop.key
• (5M) PDF: http://data.iplantcollaborative.org/quickshare/986d6b5e3cef08/2012_JCVI-CoGe-Workshop.key.pdf

Hands-on:

• Overview of CoGe's home-page
• Overview of OrganismView: Searching for genomes
  • Search for Arabidopsis thaliana TAIR v10: http://genomevolution.org/CoGe/OrganismView.pl?dsgid=11022
• Overview of GenomeView: CoGe's genome browser: http://genomevolution.org/CoGe/GenomeView.pl?z=6&x=20000&dsgid=11022&chr=1
  • Note: "Experiment" layers are in development. Show genomic quantitative measurement data.
• Overview of SynMap: CoGe's tool for pairwise whole genome comparison
  • Arabidopsis thaliana TAIR v10 v. itself: http://genomevolution.org/CoGe/SynMap.pl?dsgid1=11022;dsgid2=11022
    • Dotplot: http://genomevolution.org/r/4vot
    • Dotplot with Ks values: http://genomevolution.org/r/558m
  • Arabidopsis thaliana TAIR v10 v. Arabidopsis lyrata JGI v1:http://genomevolution.org/CoGe/SynMap.pl?dsgid1=11022;dsgid2=3068
    • Dotplot: http://genomevolution.org/r/558i
    • Dotplot with Ks values: http://genomevolution.org/r/558l
    • Dotplot with adjusted Ks values: http://genomevolution.org/r/558r
• Overview of GEvo: CoGe's for microsynteny analysis of multiple genomic regions
  • Orthologous regions: http://genomevolution.org/r/5592
  • Out-paralogous alpha regions: http://genomevolution.org/r/5591
• Overview of SynFind: Finding syntenic regions across multiple genomes
  • Arabidopsis thaliana gene v. thaliana and lyrata: http://genomevolution.org/r/5594
  • Resulting GEvo link: http://genomevolution.org/r/5593
  • Resulting GEvo link with all pair-wise comparisons: http://genomevolution.org/r/5596