1. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Methods to Compare Microbial Genomes 20 Methods to Compare Microbial Genomes Dave Ussery Biological Sequence Analysis DTU course # 27803 27 April, 2007

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

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

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

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

6. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).

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

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

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

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

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

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

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

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

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

16. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150 :749-752, (2004).

17. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Microbiology, 150 :749-752, (2004).

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

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

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

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

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

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

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

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

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

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

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

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

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

31. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU 16. Sigma Factors

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

33. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Vibrios Gamma- Proteobacteria Alpha, Beta, Delta, Epsilon- Proteobacteria Firmicutes Chlamydia Spirochaetes Actinobacteria Bacteriodes  54

34. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU # ECF Sigma Factors in 250 Bacterial Genomes Microbiology, 151:3147-3151, (2005).

35. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU 20. Secreted proteins Vibrio Microbiology, 151:1013-1017, (2005).

36. Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).

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

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