Moore Notes 4 1 09

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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?