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Using a genome to come up with questions

Using a genome to come up with questions. What’s of interest to you?. An organism? Acidimicrobium ferrooxidans ? A lifestyle? E.g., obligate autotrophs ? A process? Chemotaxis ? Carbon fixation?. Good place to start: genome paper. Any mysteries apparent in the initial annotation?.

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Using a genome to come up with questions

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  1. Using a genome to come up with questions

  2. What’s of interest to you? • An organism? • Acidimicrobiumferrooxidans? • A lifestyle? • E.g., obligate autotrophs? • A process? • Chemotaxis? • Carbon fixation?

  3. Good place to start: genome paper • Any mysteries apparent in the initial annotation?

  4. Other considerations • Length of project • One semester? • Multisemester? • What fits in well with your curriculum? • E.g., Microbial physiology class • Chemotaxis project • Central carbon metabolism

  5. Choosing a genome • Easily cultivated? • Well-studied? • Not well-studied?

  6. IMG (Integrated Microbial Genomes) http://img.jgi.doe.gov

  7. IMG • Great tool for scanning genomes • Collection of all sequenced microbial genomes • Fantastic and convenient suite of search and comparison tools • Which organisms have been sequenced? • How do I find unique things about an organism that might bear further scrutiny?

  8. IMG: Compare genomes w/heat maps Mouse over blue or red box and click on it

  9. How to find genomes that have been sequenced, and compare them using IMG

  10. IMG (Integrated Microbial Genomes) http://img.jgi.doe.gov

  11. Hit ‘find genomes’ tab (1), then hit ‘clear all’ button (2) 1 2 3 System default is for all genomes to be selected for comparison. ‘Clear all’ button makes it possible for you to select the ones you want to focus on.

  12. Hit ‘view phylogenetically’ button (3)Expand the taxa of interest

  13. Select the taxa of interest Click in the boxes next to the species names to select taxa; checkmarks will appear to indicate taxon is selected

  14. Scroll up and hit the ‘save selections’ button

  15. From here, select ‘Compare Genomes’ tab

  16. From here, hit ‘abundance profiles’ subtab

  17. Select ‘Abundance Profile Overview’

  18. Scroll down from here

  19. Select target organisms

  20. (scroll down from here)

  21. Can retrieve genes from heat map Mouse over blue or red box and click on it

  22. Genes retrieved from heat map Clicking on Gene ID number opens upgene detail page for that gene

  23. Gene detail page Gene detail page includes: nucleic acid sequence predicted amino acid sequence gene context automated annotation based on: PFAM, TIGRFAM, similarity to other genes et cetera

  24. Scroll down—gene sequence, et cetera

  25. Gene context If you mouse over the genes, the automated annotation pops up

  26. Finding questions • What’s interesting? • What’s feasible? • Shop around using • Genome papers • web tools, e.g., IMG

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