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Examples of metagenomics use cases for the Phylotastic! web tools. Presented a the Phylotastic hackathon, June 4-8 2012: http://www.evoio.org/wiki/Phylotastic
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Phylotastic! Metagenomics Use Cases
Holly Bik, UC Davis
-Omic Dictionary
• Marker gene studies – amplification of a conserved homologous gene (18S, 16S rRNA) from environmental samples
• Metagenomics – shotgun sequencing of random genomic fragments from environmental DNA
Biodiversity?
Phylogeography?
Environmental Impacts?
Extract Environmental DNA
Amplify rRNA
High-throughput sequencing
Community analysis
Diverse marine community
EASYEASY
EASY
VERY Difficult!
http://phylosift.wordpress.com
Explicitly Phylogenetic ApproachesAligned environmentalsequences
Guide Tree
Evolutionary Placement of short reads
Tree Reconciliation in PhyloSift
Environmental Sequences
Named Taxa
Pruning Subtrees from Megatrees
• User inputs a list of reference sequences with NCBI Taxon IDs Pulls down tree topology
• Unclassified sequences in a reference phylogeny could be “named” with the most appropriate higher level taxon
Name Matching and TNRS
• Different taxonomic synonyms have different NCBI taxon IDS– Shigella: 620 and E.coli: 562– Species/genus boundaries still debated
• TNRS would provide a “matrix” for standardizing IDs– E.g. E.coli/Shigella supergroup: 12345
Integrating Comparative Data
• Metadata is a standard part of any well-constructed metagenomics study
– Depth (marine samples)– Aquatic/Terrestrial– Temperature– pH– Dissolved Oxygen
Integrating Comparative Data
• Metadata also includes information about the sequences themselves
– Abundance information– Distribution across sample sites
Branch thickness can be incorporated into XML tree files and visualized within Archaeopteryx
Mashup with Online Data
• Pull down NCBI metadata for a given reference sequence accession
– Habitat metadata – Ecological associations –e.g. symbionts– Genome availability– Related publications– Pictures, etc. would be awesome
Exploring Trees
Ecologically, what are these reference taxa doing??
Pertinent info for biological interpretations of DNA data!!
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