1) Go to TIGR's Comprehensive Microbial Resource (CMR). Note, CMR was optimize for use with Netscape since Netscape adheres to WWW standards and Microsoft IE does not. If the results do not look right, try this on Netscape instead of IE.
2) Click on the tab at the top that says "Align Genomes". For the X-axis, choose Buchnera sp. APS (this is the bacterial symbiont that provides aphids with amino acids). For the Y-axis, choose E. coli K-12 (this is the type that lives in your gut now and is not harmful). Given that Buchnera is believed to have descended from a common ancester of E. coli, do these geneomes align the way you might expect? Explain your answer and why the alignments look the way they do.
3) As a comparison, go back to the Align Genomes page and click on the link that says "E. coli 0157 vs. E. coli K12" which compares the pathogenic strain 0157 with the non-pathogenic strain. How similar are these two genomes? What two striking features are evident at this level? Click on the big green bar in the smaller window to zoom in on this region. Is the green bar continuous?
4) At the bottom of the Comprehensive Microbial Resource, find "Genome v/s Genome Protein Hits". First, choose E. coli K-12 as the reference genome. Second, choose Buchnera from the popup menu and then click on the “Add Molecule” button. Choose E. coli K-12 and then “Add Molecule”. This will allow you to compare the encoded proteins (as defined by the published annotations). Click on “Generate Display”. The results are provided graphically (left side) and in text format (right side). If you mouse over the graphic displays of the genomes, you can see where the similarities lay within the reference genome. Knowing that Buchnera has 583 ORFs and E. coli has 4,288, do the results of this comparison match your expectations?
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