1. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Dave Ussery Biological Sequence Analysis DTU course # 27803 15 April, 2005

2. Center for Biological Sequence Analysis The Technical University of Denmark DTU

3. Outline Introduction Genome (DNA properties) Transcriptome (RNA properties) Proteome comparisons 15 methods (!)

4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Lars Bacteria are very small! Tim Tine Mette Bjørn Kristoffer Anne Peter Heng Natasja Hanni Lars Lise Nikolaj Tom

5. Center for Biological Sequence Analysis The Technical University of Denmark DTU Warning - you’ve already seen some of this before!

6. Center for Biological Sequence Analysis The Technical University of Denmark DTU rRNA tree

7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Biological info.? Genome Comparisons 1. Chromosome alignment

8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150:2491- 2493, (2004).

9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150:513-515, (2004).

10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 3. AT content Microbiology, 150:749-751, (2004).

11. Center for Biological Sequence Analysis The Technical University of Denmark DTU 3. AT content Bioinformatics, 20:3682-3686, (2004).

12. Center for Biological Sequence Analysis The Technical University of Denmark DTU

14. 3. AT content - globally Microbiology, 150:749-752, (2004).

15. Center for Biological Sequence Analysis The Technical University of Denmark DTU 3. AT content - locally Microbiology, 150:749-752, (2004).

16. Center for Biological Sequence Analysis The Technical University of Denmark DTU Bioinformatics, 20:3682-3686, (2004). Genome Comparisons 4. Oligomer skews

17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Environmental Microbiology, in the press, (2005)

18. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 151:633-637, (2005).

19. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 5. Repeats Microbiology, 150:3519-3521, (2004).

20. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150:3899-3903, (2004).

21. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 6. tRNAs and codon usage Microbiology, 150:1603-1605, (2004).

22. Center for Biological Sequence Analysis The Technical University of Denmark DTU

23. Genome Comparisons 7. bias in codon usage Microbiology, 150:1603-1605, (2004).

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

25. Genome Comparisons 8. amino acid usage Microbiology, 150:1603-1605, (2004).

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

27. Genome Comparisons 9. Promoters Microbiology, 150:2791-2793, (2004).

28. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 10. Annotation quality Trends in Genetics, 17:425-429, (2002).

29. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons Trends in Genetics, 17:425-429, (2002).

30. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons Trends in Genetics, 17:425-429, (2002).

31. Center for Biological Sequence Analysis The Technical University of Denmark DTU Trends in Genetics, 17:425-429, (2002).

32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150:2791-2793, (2004).

33. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 11. Blast atlases Microbiology, 150:3091-3093, (2004).

34. Center for Biological Sequence Analysis The Technical University of Denmark DTU BMC Genomics, 4:12, (April, 2003).

35. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 12. Proteome comparisons Microbiology, 151:1-4, (2005).

36. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 13. 2-D comparisons Microbiology, 151:333-337, (2005).

37. Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 151:333-337, (2005).

38. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 14. Secreted proteins Microbiology, 151: in the press, (2005).

39. Center for Biological Sequence Analysis The Technical University of Denmark DTU Nature Reviews Microbiology, manuscript in preparation (2005).

40. Center for Biological Sequence Analysis The Technical University of Denmark DTU 15. Transmembrane helices

41. Center for Biological Sequence Analysis The Technical University of Denmark DTU helices Proteobacteria Firmicutes

42. Center for Biological Sequence Analysis The Technical University of Denmark DTU Nature Reviews Microbiology, manuscript in preparation (2005).

43. Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Comparisons 15. Transmembrane helices Nature Reviews Microbiology, manuscript in preparation (2005).

44. Center for Biological Sequence Analysis The Technical University of Denmark DTU

46. Summary 1. I’ve listed 15 ways to compare genomes. summary 2. Within a few years, there will be more than 1000 bacterial genomes to compare.