Moore Notes 5 15 13

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Group Call

  • Participants: Katie, Josh, Tom, Stephen, Dongying
  • Annotating SFams
    • Got annotation file from JGI
      • Dongying: file not bigger than previous one
      • Tom: will try using this for now, but Tim has Interpro running on the cluster
        • backup plan, or for next update
    • Stephen: building HMMs for KEGG Orthology groups
      • Lots of sequence length variation within groups
      • For genome annotation, he is filtering out long sequences
      • What do we want to do for annotating SFams?
        • Alternative to HMMs would be to pairwise search
        • E.g., BLAST or RAPSearch vs. ALL KEGG annotated sequences (including very long or short ones)
        • Tim will compare and we can decide from there
    • EggNog and KEGG both have some sequences in more than one ortho group
      • Stephen: may be due to fusion proteins
        • Dropping these for simulations
        • Dongying: dropping might not be a good idea
  • Tom talk to Victor Hansen-Smith from Sandy Johnson's lab
    • Amino acid substitutions that alter function in a gene family
    • Idea: use his ancestral sequence distributions to search SFams
    • Another idea: unannotated SFams (not connected in SFam network) to study de novo gene creation
      • Rates, patterns on tree, etc.
  • Josh: problems in soil niche modeling
    • Tibetan soil study
      • local data: C:N predictive of diversity, pH not (contrary to studies in other places)
      • raster data: pH is correlated with diversity
    • Check local vs. raster for other variables
    • Compare range of local values in Tibet versus N America (same for rasters)
    • Tom: C:N is important in mycology biomass
  • June 17 meeting agenda
  • Josh and Stephen headed to ASM in Denver