Moore Notes 7 31 13

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
    • Sarah: Is this enough?
    • Tom: We used 20 million for human microbiome and some published studies used much less
    • Josh: Tara is doing 100 million, probably in order to do assembly
    • Katie: prairie soils used average of 12 million paired end reads per sample
    • Relevant paper: http://www.nature.com/srep/2013/130611/srep01968/full/srep01968.html
  • 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