Moore Notes 7 30 08

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Group Call 7-30-08 Called in to AT&T conference


  • Green Lab
    • Jessica Green
    • James O'Dwyer
    • Steve Kembel
  • Pollard Lab
    • Katie Pollard
    • Josh Ladau
    • Sam Riesenfeld
  • Eisen lab
    • Jonathan Eisen
    • Dongying Wu
    • Srijak Bhatnagar
    • Marisano James

Mechanism of conferences

  • Still looking for the ideal system to do video and audio chats
  • Biweekly meetings
    • Miniupdates
    • And then maybe a longer update by some groups


  • Katie update on CiteYouLike
    • Created iSEEM group
    • Katie will post details on how to use it online
    • Everyone should use it


  • Everyone said 1 sentence about themselves

Flow chart

  • Eisen summarizes flow chart
  • Dongying summary of gene families
  • Eisen summarizing big picture of the project

General questions

  • Eisen answering questions about many things
    • Why rRNA not perfect?
      • Metagenomics generates few rRNA sequences - need to use other thigns
      • Extensive copy # variation
      • Too low sequence variation for some question
    • What are the precomputes we are doing?
      • Copy number variation
      • Universality
      • Gene tree vs. species tree
      • Sequence conservation
      • Generating HMMs
    • Should OTUs be by percent identity or something else like ecotypes or phylogeny?
      • Phylogeny probably better
      • Ecotypes only works with very abundant organism
  • Green questions about rare sequences - How can you ID/bin them? Eisen answered
    • Blast match to VERY closely related sequence
    • Phylogeny (building a phylogenetic tree of the sequence with a useful phylogenetic marker gene can help determine what type of organism the sequence came from)
      • This is what Eisen did with the Glassy winged sharpshooter symbionts
  • What about abundant organisms?
    • Green pointed out that Steven G. does different things with SAR11. This is because it is highly abundant in the data sets he is looking at.
    • Can bin by lots of methods
    • Examples include assembly, reference genome alignment, composition, depth of coverage, etc.