Moore Notes 3 12 13

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?