Moore Notes 2 5 14

Group Call

• Participants: Katie, Tom, Patrick, Sarah, Ladan, Dongying, Stephen

• Tom: looking for a db of 16S sequences
  • Desired features
    • Clustered into OTUs or taxonomically annotated
    • With abundances
    • Annotated by samples
  • HMP has an OTU table
  • So does MICROBIS
  • Stephen: see paper by Mihai Pop http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html
  • No cross-study databases

• Katie: Update on bioinformatics hire
  • Interviewing candidates in next few weeks

• Stephen: MicrobeDb is up an running

• Stephen: Check out SIMAP http://boincsimap.org/boincsimap/
  • All-vs-all blast (like) search results
  • Paper: http://nar.oxfordjournals.org/content/early/2013/10/26/nar.gkt970
  • What are benefits of having our own family resource? e.g., versus EggNOG (uses subset of SIMAP)
    • Versus spending time/resources on other research
    • Tom: SFams HMMs are probably more stable over time than de novo clustered protein families
    • Stephen: Incorporating metagenomic data
    • Stephen: Ecosystem/environment specific protein databases
    • Katie: RNA gene families
    • Katie: Viral gene families

• EFI update from Katie

• Upcoming meetings
  • No call on 3/12
  • Sarah will present 2 weeks from now