Moore Notes 3 12 13

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Group Call

  • Participants: Katie, Stephen, Dongying, Josh, Guillaume, Tom
  • Guillaume: data updates
    • Mary Ann Moran
      • Eight projects, 40 samples or more
      • Put data on edhar and made some notes about them on iSEEM2 OWW site
      • Georgia and California coast
    • Will look for other data sets on CAMERA
      • Viral metagenomes
      • Other GBMF researchers by name
  • Josh: ocean model data as variables in niche modeling
    • Jon Zehr from UCSC
  • Stephen: MRC simulations from genomes
    • Picking genomes with maxPD on 16S FastTree tree
      • Some taxa don't cluster with their annotated phylum (from IMG)
      • Some taxa have really long branch lengths
    • Dropping taxa that don't cluster with annotated phylum, as well as those with long branches (e.g., >0.1 or 0.2)
    • Loose a couple phyla - is this OK?
    • Donying: Could be sequence orientation problem
  • Guillaume visiting Gladstone on Monday 3/18
    • Will be working with Tom on SFams updating software
  • Dongying: treeOTU
    • New method to define OTUs using proteins markers rather than 16S
    • Distance rule that works for 16S doesn't work for diverse set of protein markers with different rates of evolution
    • Approach is to group sequences into OTUs using tree for each marker
      • Provides a single definition for all markers
      • Alternative to defining marker-specific PID thresholds
    • To select the tree-cutting threshold (PN), used adjusted mutual information (e.g., versus 16S mothur OTUs)
      • Can find a PN value that produces clusters very similar to average linkage mothur clustering of 16S
      • Can find PN values that more closely recapitulate annotated taxonomic groups
    • See slides for details
  • Novel structures in SFams?