Moore Notes 7 31 13

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Group Call

  • Participants: Katie, Jonathan, Tom, Stephen, Donying, Sarah, Josh, Guillaume
  • SFams issues revealed through MRC simulations
    • Tom and Stephen will work on troubleshooting, coordinating with Dongying and Guillaume
    • Discuss on future call if needed
  • EMP sequencing
    • Costs
      • BGI: $570/sample
      • ANL: $247/sample (cheaper $99 library prep)
    • Coverage: 10 million 100bp paired-end reads per sample
    • Get quotes for 250bp paired end reads
    • Katie working to get list of locations from Gilbert lab
    • Josh will then coordinate with Alexis at Tara project to try to do complementary samples
  • Functional extinction idea
    • Similar to A.P. Martin's idea of looking at organisms on long branches on trees because they harbor more unique functions
    • Are there synapomorphies?
      • LGT decreases the prevalence of this.
      • But if LGT is geographically restricted, there will still be
    • Eukaryotic (less LGT?) versus prokaryotic (more LGT?) rates
    • Josh: some papers on this topic in macroorganisms
    • Related to impact of climate change on functional diversity
    • Sarah: what about redundancy of functions over several gene families or pathways
  • KEGG annotation of SFams
    • Tim L used same approach as we used for InterPro
    • Most KEGG-SFams mappings are 1-to-1
    • Can link SFams together into pathways
    • Further grouping into processes