User:Morgan G. I. Langille/Notebook/Project management

Halophiles

Erin and Andrew getting ortholog sets all halophile genomes Need to make list of things to be done for roche genome paper.

1. Re-do crispr analysis for new NCBI genomes.
2. Look at homologs of genes identified in new Science metabolic paper.

Darpa

• phone call on Friday

Erebus

• got matrix and built cluster using vegdist
• need to think about ways to identify pfams that have different counts to each other and to whole genomes.
  • take pfam counts from all completed genomes, get a distribution, then ask if a single count is normal or not taking into account mutiple test correction

Protein family stuff with Steve

• Need to re-write R scripts to calculate correlations and ecological distances from matrix (this needed for erebus project as well).
  • Look at online notebook for some code, as well as darpa wiki (for the correlation stuff). I emailed steve asking for his R scripts.

Rough Ideas

Starting with PFAM counts across all GOS samples

• Looking at samples
  • alpha diversity of GOS samples (measure total protein diversity in each sample)
    • provide a listing of most diverse samples and indicated if those are environmentally related
  • beta diversity of GOS samples (are the samples related...presumbly yes)
    • show a tree and possible a network describing the relatedness of the samples
  • estimate total number of different protein families for each sample and all samples combined using chao index?
• Looking at families
  • alpha diversity. what fams are the most rich (not that interesting), diverse (interesting and informative)
    • provide list of most diverse families and maybe suggest why those are so diverse?
  • beta diversity -> do the groupings tell us anything (e.g. are they similar function, similar localization, etc.)
    • map to GO terms to see if similar function
  • chao index
    • estimate total number of proteins for each family in the ocean (what is the most prevalent)

Collaboration with Steve would be a comparison between diversity measurements using taxon vs phylogenetic vs functional