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

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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

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

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

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

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).

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

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

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

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

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? Comparison tool #1 - The table

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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: , 2000

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

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

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

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

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

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

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

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

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

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

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

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

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.)