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