User:R. Eric Collins/GenomicsTutorial

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What... is your Quest?

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

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