This project tracts the human microbiome
16s sequencing ribosomal, gives taxonomic name tags.
Software (available for download):
BLASTs sequences to identify genes.
Includes each gene using its weighted average BLAST score
Assigns genes to pathways
under restraints of minimum parsimony
and taxonomic limitation
smooths (data is counts, so Witten-Bell smoothing)
+ a few more steps (gap filling)
Results:
For any given environment (tooth, gut, etc.), the same basic pathways are present at about the same abundance, but the species/taxons vary greatly in abundance.
Further, all pathways/functions available everywhere, with local enrichment for those which are locally usefull.
software/links
huttenhower.sph.harvard.edu
Look for Valm et al PNAS 2011 on the tooth metagenome
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