Moore Notes 2 18 09

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Group Call

  • GBMF needs more detail on UCSF expenditures for annual budget
  • Eric Matson (Berkeley) and Robin Kodner (from Ginger Armbrust's Lab, UW) are visiting Eisen lab
    • they are working on metagenomic phylogenetics
  • Update from James
    • spatially explicit taxanomic predictions (building on PNAS paper)
    • stochastic processes and allometric scaling
    • unified neutral theory (taxa area relationships/distance decay, two-point correlations)
      • JE: How will the predictions be tested with metagenomic data?
      • problems: measuring area, can't count everything (and undersampling is a function of area/volume)
      • Finley Science paper: protist analysis that uses every species and whole environment as a data point
    • Josh is working on similar things, and we will follow up in a separate call
    • Taxa-individual relationships (rarefaction)
    • Distance-decay may be more feasible (undersampling is still an issue, may be different for z)
  • Simulations
    • Which taxa? How many?
    • How to choose taxa? Are they in AMPHORA?
      • reliably placed ones
      • Dongying's phylogenetic distance (evenly sampled from tree) - simple case for tree building
      • to look like metagenomics data (clusters)
      • include archaea?
    • Complete sequences vs. complete with fragments
    • What gene(s)? Need full length alignments - complete data answer
      • 16S rRNA (metagenomic vs. full length)
      • RecA or some faster evolving gene (can build HMM with ZORRO)
      • 2 AMPHORA markers (31 HMMs for key markers), e.g. longest and shortest
    • DNA vs. codon vs. amino acid
      • Answers depend on the use of the simulated data
    • How to make alignments?
    • What does pool of reads look like?
      • to start, one read per taxon not overlapping - does it get placed on the full tree correctly?
      • same, but with overlapping reads
      • mulitple reads non-overlapping per taxon - do they place the reads together?
      • mix of rare (not overlapping) and abundant taxa (overlapping)
    • Problem: how to assess trees when leaves vary between them?