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  1. Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU Page 1 Comparison of sequenced Bacterial Genomes Dave Ussery Advanced Bioinformatics course lecture 21 November, 2003

  2. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Overview overview Last week: DNA structures in Bacterial Genomes Today: How do you cp. 150 genomes? Introduction & a look at 4 Pseudomonas genomes 5 epsilon Proteobacteria (Campylobacter, Helicobacter, and Related Organisms) 3. Comparison of 5 Clostridium genomes

  3. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group title Part 1: Introduction And A look at 4 Pseudomonas genomes

  4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group overview OVERVIEW Introduction to Bacterial Genome cp. An example of “Current methods” (Bordetella) Comparison of Four Pseudomonas Species [CBS tools for bacterial genome comparison]

  5. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Introduction 3 Bordetella genomes Example: 3 Bordetella genomes Parkhill et al., Nature Genetics, 35:32-40, (2003).

  6. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Wheel plots

  7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Genome alignment

  8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group circles

  9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Comparing Genomes Comparing genomes: 1. Table for comparisons 2. Atlas plots for visualisation of the whole chromosome • Genome Alignment (sometimes useful) 3. Proteome comparisons

  10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group How do you compare more than 100 bacterial genomes? Cp 100 genomes Comparison tool #1 - The table http://www.cbs.dtu.dk/services/GenomeAtlas/Bacteria

  11. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Repeats table

  12. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group repeats

  13. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Purine stretches

  14. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Genome Letters

  15. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Di and Tetranucleotides

  16. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group GL tables 1 and 2

  17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group REP logos Repetative sequences REP REP REP REP

  18. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group GL Figure 10

  19. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group GL Table 3

  20. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Know your insects

  21. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Paer. Genome atlas Comparison tool #2 - DNA atlases

  22. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Pput Genome Atlas

  23. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Psyr. Genome Atlas

  24. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group 3 genome alignment

  25. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Table 2

  26. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group sigmas

  27. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Sig70 tree

  28. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Blast table Comparison tool #3 - Proteome cp.

  29. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Blast atlas

  30. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Paer blast atlas

  31. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Pput blast atlas

  32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Psyr blast atlas

  33. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group zoom

  34. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Table 3.1

  35. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Phylome 1 atlas

  36. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group phylome2atlas

  37. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group An aside An aside… Bacteria has a periodicity of 11 Archaea has a periodicity of 10 Peder Worning et al., Nucl. Acids Res., 28:706-709, 2000

  38. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli autocorrel.

  39. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli autocorrel

  40. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Fourier transform

  41. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli O157

  42. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli periodicity

  43. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Haemophilus

  44. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. jejuni

  45. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H.pylori J99

  46. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group M. janasschii

  47. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group T. maritima

  48. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cp. 3 genomes

  49. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Pseudomonas periodicity

  50. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group summary Summary 3 ways to compare genomes: 1. Table (gives single-value, general features) 2. DNA Atlases (circular maps of the whole chromosome) 3. Proteome comparison (Blast, Phylome-atlas, etc.)