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Page 1 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparison of sequenced Bacterial Genomes Comparative Microbial.

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Presentation on theme: "Page 1 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparison of sequenced Bacterial Genomes Comparative Microbial."— Presentation transcript:

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

2 overview Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU Overview Last week: DNA structures in Bacterial Genomes Today: How do you cp. 150 genomes? 1.Introduction & a look at 4 Pseudomonas genomes 2.5 epsilon Proteobacteria (Campylobacter, Helicobacter, and Related Organisms) 3. Comparison of 5 Clostridium genomes

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

4 OVERVIEW 1. Introduction to Bacterial Genome cp. 2. An example of “Current methods” (Bordetella) 3. Comparison of Four Pseudomonas Species [CBS tools for bacterial genome comparison] overview Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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