Moore Notes 1 16 13

Group Call

• Participants: Jonathan, Katie, Dongying, Guillaume, Stephen, Josh

• Guillaume: updating SFams
  • Downloading new genomes (>2000, about 5000 total)
  • Doing sifting
  • All-vs-all LAST for MCL of new sequences next
    • Stephen: LAST designed for "best hit" searches
    • Maybe the m-parameter will produce a distance matrix that is too sparse or not symmetric
    • Katie: Compare results to BLAST for sequences that we had previously

• Stephen: SFam clans
  • Currently use consensus sequence (regardless of family size)
  • Another distance might be better
    • PRC is a good profile-vs-profile method, but very slow
    • SCOOP looks like a good option
    • Dongying: Could compute multiple consensus sequences per family for larger families

• Stephen: classification thresholds
  • Min scoring true positive, max scoring false positive
  • Best if these don't overlap, but sometimes they do
  • In PFAMs, the false positives above the min true positive threshold are all from a related family (by definition)
  • Stephen investigated this in SFams (5%), PFAMs (6%), TIGRFAMs (3%)
  • Round 2 genomes analysis shows that these problematic families are very common
  • Family-specific thresholds might be a good idea, though makes it more complicated

• Stephen: hmmsearch performance
  • More sensitive than BLAST for full-length sequences
  • But metagenomics data (i.e., short sequences) is better classified using BLAST/LAST
    • Not specific to SFams
    • Particularly true for large families
  • Need to increase read length to find inflection point
  • Sequencing error is not a major factor

• Need a better and update web presence
  • Jonathan: Word Press has website/blogging software
    • Open, self-install version (.org) needs to be hosted on a server (e.g., dreamhost)
    • Commercial version (.com) is hosted, free for a little storage, $20/year for more
  • Will have iseem.org point there
  • Keep notes and private pages on OWW for now

• Dongying: Statistical question
  • How to compare clusters?