Moore Notes 4 1 09

Group Call

• Progress Report was due Monday (now Friday)
  • OK if not much to add since annual report
  • JE will start wiki page
  • We should all add what we're up to (~ paragraph per postdoc, plus sections on presentations, pubs, etc)

• Simulations
  • Do we have a place to put data/code set up yet?
    • Every one needs to send their logins to Srijak
  • format for alignments (Stokholm?)
    • Dongying has alignmentformt.pl script
  • Martin uses E-entrance from NCBI
  • profile HMMs from AMPHORA
    • Which alignments are used?
    • Why Smith-Waterman?

• Sample size issue (posted on collectiveX)
  • AMPHORA on Delong: mean number of sequences is only 2
    • versus Sargasso Sea (1.2 million sequences)
    • Future studies will have 50,000 sequences or more
  • Could look at more genes (still won't change depth of coverage per gene)
    • Different types of genes - they will have different profiles across the landscape
  • Combine genes. How?
    • Concatenated alignment of all 31 markers for fully sequenced genomes, then place reads on this "genome" tree
  • Could try other data sets
  • For presence/absence
    • what resolution?