1. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 20 Methods to Compare Bacterial Genomes Dave Ussery Biological Sequence Analysis DTU course # 27803 15 May, 2006

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

3. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Peter

4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group

5. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Proteobacteria E. coli Salmonella Vibrio Bacillus Staphylococcus Streptococcus Chlamydia Cyano- bacteria Firmicutes Functional & Integrative Genomics, in the press, to be published June, 2006. Du står her

6. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 2. Number genes [coding density] 3. AT content 6. Repeats 4. Oligomer skews 5. Chromosome alignment 8. tRNAs and codon usage 9. Bias in codon usage 10. Amino acid usage 1. Length 7. Periodicity Genome Coding 20 Methods to Compare Bacterial Genomes

7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 14. Proteome comparisons 13. Blast atlases 12. Annotation quality 15. 2-D correlation of properties 16. Sigma Factors 17. Two-component systems 18. Transcription Factors 19. Membrane Proteins 20. Secreted Proteins 11. Promoters

8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 1. Length

9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 3. AT-content

10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group

11. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Friis, Jensen, and Ussery

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

13. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Eva

14. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Bioinformatics, 20:3682-3686, (2004).

15. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 日欧先端科学セミナー ” 機能的ゲノム学 ” フォローアップワークショップ ２００６年３月８日 Heng

16. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 11. Promoters Microbiology, 150:2791-2793, (2004).

17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group tRNAs and codon usage Microbiology, 150:1603-1605, (2004). Peter

18. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Clavibacter michiganensis 27% A+T content Nitrococcus oceani 50% A+T content Wigglesworthia glossinidia 78% A+T content

19. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Hanni Soil BacteriaGram +MollicutesEnterics

20. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group amino acid usage Microbiology, 150:1603-1605, (2004).

21. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Diagnosis, epidemiology and antibiotic resistance of the genus Clostridium, (Duchesnes C., Mainil J, Pelkonen S. and Menozzi MG, editors), Proceedings of the meeting, Presses de la Faculté de Médecine Vétérinaire de l'Université de Liège, pages 60-66, (2004). 4. Oligomer skews

22. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Bioinformatics, 20:3682-3686, (2004). Peder Lars

23. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Peder Worning and Lars Juhl Jensen et al., Environmental Microbiology, 8:353-361 (Feb. 2006)

24. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group geneC Replication Origin Replication Terminus geneA geneB geneA doubling time

25. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group t D > 60 min. C = 50 min. t D = 40 min. C = 50 min. t D = 20 min. C = 50 min. A.

26. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 3x 2x 3x Escherichia coli strain K-12_W3110 Replication Origin Bacillus thuringiensis strain 9727 Treponema denticola strain ATCC35405 Mycoplasma genitalium strain G37 3x Photobacterium profundum strain SS9

27. # 16S rRNAs

28. # tRNAs

29. Signal / Noise ratio

30. Gene skew (%)

31. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Proteobacteria E. coli Salmonella Vibrio Bacillus Staphylococcus Streptococcus Chlamydia Cyano- bacteria Firmicutes Buchnera Burkholderia Pseudo- monas Xantho- monas Agrobact. Campy. Helicobact. Bacteroides Mycoplasma

32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group What have we learned from 300 sequenced bacterial genomes? 1. Genetic diversity is greater than we thought. 4. Generally G’s are biased towards the leading strand, but the strand bias of A’s is tax-specific. 2. Very large genomes tend to be GC-rich, whilst small genomes tend to be AT-rich. 3. There are patterns, both locally and globally of AT-richness in bacterial chromosomes.

33. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 12. Annotation quality Trends in Genetics, 17:425-429, (2002).

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

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

36. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Microbiology, 150:3899-3903, (2004). 6. Repeats

37. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 15. 2-D comparisons Microbiology, 151:333-337, (2005).

38. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Microbiology, 151:333-337, (2005).

39. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group BMC Genomics, 4:12, (April, 2003). Blast Atlases

40. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 11. Blast atlases Microbiology, 150:3091-3093, (2004).

41. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group P1 P2 P3 P4

42. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Kristoffer

43. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Jannick Microbiology, 151:1013-1017, (2005).

44. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group 日欧先端科学セミナー ” 機能的ゲノム学 ” フォローアップワークショップ ２００６年３月８日 Jannick

45. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group