Moore Notes 7 30 08

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

Participants

• 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

CiteYouLike

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

Introductions

• 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.