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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

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

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Comparison of sequenced Bacterial Genomes

Comparative Microbial Genomics Group

Dave Ussery

Advanced Bioinformatics course lecture

21 November, 2003

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overview

Comparative Microbial Genomics Group

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OverviewLast 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

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title

Comparative Microbial Genomics Group

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Part 1: Introduction

And A look at 4 Pseudomonas genomes

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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

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3 Bordetella genomes

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Introduction Example: 3 Bordetella genomes

Parkhill et al., Nature Genetics, 35:32-40, (2003).

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Wheel plots

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Genome alignment

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circles

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Comparing Genomes

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Comparing genomes:

2. Atlas plots for visualisation of the whole chromosome

• Genome Alignment (sometimes useful)

1. Table for comparisons

3. Proteome comparisons

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Cp 100 genomes

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Comparative Microbial Genomics Group

How do you compare more than 100 bacterial genomes?

Organism perAT lengthPseudomonas aeruginosa, strain PAO1 33.4 6,264,403Pseudomonas fluorescens SBW25 40.0 6,703,654Pseudomonas putida KT2440 38.5 6,181,863P. syringae pv. tomato strain DC3000 41.0 6,397,126Average of 150 genomes 52.8 3,004,048

http://www.cbs.dtu.dk/services/GenomeAtlas/Bacteria

Comparison tool #1 - The table

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Repeats table

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Organism Global Direct Global InvertedLocal Direct Local InvertedP. aeruginosa PAO1 3.6 2.5 12.1 7.7P. fluorescens SBW25 3.8 3.2 6.5 4.5P. putida KT2440 4.7 3.8 7.1 5P. syringae DC3000 6.9 6.2 5.2 3.8Average of 150 genomes 4.1 2.9 8.3 6.1

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repeats

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Purine stretches

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Genome Letters

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Di and Tetranucleotides

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GL tables 1 and 2

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REP REPREPREP

Repetative sequences

REP logos

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GL Figure 10

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GL Table 3

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Know your insects

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Paer. Genome atlas

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Comparison tool #2 - DNA atlases

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Pput Genome Atlas

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Psyr. Genome Atlas

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3 genome alignment

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Table 2

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Organism perAT length rRNA operons # genes # sigmasPseudomonas aeruginosa, strain PAO1 33.4 6,264,403 4 5566 23Pseudomonas fluorescens SBW25 40.0 6,703,654 5 5480 29Pseudomonas putida KT2440 38.5 6,181,863 7 5350 23P. syringae pv. tomato strain DC3000 41.0 6,397,126 5 5471 14Average of 150 genomes 52.8 3,004,048 3 2890 8

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sigmas

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Sig70 tree

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Blast table

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Comparison tool #3 - Proteome cp.

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Blast atlas

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Paer blast atlas

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Pput blast atlas

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Psyr blast atlas

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zoom

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Table 3.1

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Phylome 1 atlas

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phylome2atlas

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An aside

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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

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E.coli autocorrel.

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E.coli autocorrel

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Fourier transform

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E.coli O157

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E.coli periodicity

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Haemophilus

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C. jejuni

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H.pylori J99

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M. janasschii

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T. maritima

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Cp. 3 genomes

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Pseudomonas periodicity

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Summary

1. Table (gives single-value, general features)

summary

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2. DNA Atlases (circular maps of the whole chromosome)

3 ways to compare genomes:

3. Proteome comparison (Blast, Phylome-atlas, etc.)