Moore Notes 7 24 13

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Group Call

  • Participants: Katie, Jonathan, Ladan, Sarah, Dongying
  • Josh's visit to Davis went well. Great talk. He should go on the job market.
  • VIROME: Eric Wommack
    • Virus diversity
    • Developed a bioinformatics pipeline because there weren't tools out there
    • Primarily a virus biologist, oceanographer
    • How applicable are VFams to marine microbiology?
      • Many sequenced viruses have mammalian or well-characterized bacterial hosts
      • Eric probably mostly interested in phage
    • Giant viruses are mostly marine
      • If some one does size fractioning, then these will end up in bacterial and eukaryote fractions
      • Their genomes are very divergent
  • What about eukaryote protein families?
    • Tom and/or Holly may want to work on this
    • Eukaryotic diversity is bad in genome databases
    • Should have photosynthetic algae (not closely related to plants), but none have genomes yet
    • Could be a good test case for seeing how using metagenomes or assemblies from metagenomes work for building protein families
      • Good options for interactions with other GBMF labs
      • Ambrose is doing some diatom genomes, which could be used for validation of the metagenome-based families idea
  • EMP samples
    • Talked with Jack Gilbert last week
    • Got quote for sequencing with them
    • Jonathan will get a quote from BGI, his lab could potentially do the library prep
    • Jack's group will be sending information about samples
      • Would be cool to do coastal, but environmental rasters are probably not fine enough resolution
      • Open ocean, maybe geographically restricted (e.g., the pacific), would be better