User:R. Eric Collins/GenomicsTutorial

What... is your Quest?

• What do you want to get out of this tutorial?

• chalkboard of our examples
• online Genomics resources

Molecule

• What is your favorite biomolecule?
  • sarcosine
  • sulfate
• What questions do you have about this biomolecule?
  • What biochemical pathways is it involved in?
    • KEGG Pathways/MetaCyc

Biochemical pathway

• What is your favorite biochemical pathway?
  • compatible solute metabolism
  • sulfate reduction
• What questions do you have about this pathway?
  • Example: Is sulfate reduction encoded by the microbial community living in Octopus Hot Spring in Yellowstone National Park?
    • IMG/M --> KEGG KAAS

Gene

• What is your favorite gene?
  • soxBDAG -- sarcosine oxidase
  • apaA -- dissimilatory sulfite reductase
• What questions do you have about this gene?
  • Example: Is selection acting on the apaA gene involved in dissimilatory sulfite reduction?
    • KEGG Pathways --> IMG Functions --> HyPhy
  • Is there evidence for the horizontal transfer of ice-binding gene in Colwellia?
    • NCBI Proteins/IMG + RDP/greengenes/SILVA --> iToL

Microorganism

• What is your favorite microorganism?
  • Colwellia 34H
  • Desulfovibrio vulgaris
• What questions do you have about this microorganism?
  • Example: What are the differences between the wild type and my mutated strain of Desulfovibrio vulgaris?
    • NCBI Genomes --> Galaxy

Environment

• What is your favorite environment?
  • sea ice
  • mud
• What questions do you have about the microorganisms inhabiting this environment?
  • How does the prokaryotic diversity in the western Chukchi Sea change between summer and winter?
    • VAMPS
  • Is phage diversity significantly different between winter and summer sea ice?
    • CAMERA --> Alpha/Gamma Diversity