Moore Notes 11 4 08

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All Group Call

  • New personnel: Josh, Sam and Steve all started
  • OWW site
    • Every one should add their photo and edit their text
    • Steve Green will pick some photos of microbes
  • Within lab iSEEM meetings
    • Green lab iSEEM people will meet weekly
    • Pollard lab will try the same
  • Authorship of papers
    • JG suggested trying to avoid arguments over paper authorship within team
    • Idea: discuss authorship plan near start of a project
  • Discussion of Wu & Eisen (2008) paper
    • Summary by Martin
      • Marker genes: single copy, housekeeping
      • ClustalW -> profile HMM
      • Manually curate (mask)
      • Concatenate genes
      • Build species tree
      • Application to metagenomics: align read to profile and mask, rebuild tree with present bases (constrained by topology of species tree), assign taxonomy (level that can be resolved depends on density of sequenced genomes in that part of the tree)
      • Could estimate rates of evolution and do tests (with caveat of masking leading to more conservation - maybe use unmasked alignments?)
    • Output: family members, alignments, individual gene/read trees, taxon assignments (with reliability)
    • Future work:
      • More genomes?
      • More marker genes?
      • Sensitivity to genomes, genes
      • Automated mask building
      • Processing and tree building with multiple reads (how to handle cases where they hit in different parts of the profile?)