center for biological sequence analysis the technical university of denmark dtu comparative...

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Comparative Microbial Genomics

Dave UsseryBiological Sequence AnalysisDTU course # 2780315 April, 2005

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Outline

• Introduction• Genome (DNA properties)• Transcriptome (RNA properties)• Proteome comparisons

15 methods (!)

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Bacteria are very small!

Tim

TineMette

Bjørn

Kristoffer Anne

Peter

Heng

Natasja

Hanni

Lars

Lise

Nikolaj Tom

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Warning - you’ve already seen some of this before!

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rRNA tree

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Comparative Microbial Genomics Group

Biological info.?

Genome Comparisons

1. Chromosome alignment

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Microbiology, 150:2491-

2493, (2004).

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Microbiology, 150:513-515, (2004).

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Genome Comparisons

3. AT content

Microbiology, 150:749-751, (2004).

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3. AT content

Bioinformatics, 20:3682-3686, (2004).

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3. AT content - globally

Microbiology, 150:749-752, (2004).

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3. AT content - locally

Microbiology, 150:749-752, (2004).

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Bioinformatics, 20:3682-3686, (2004).

Genome Comparisons4. Oligomer skews

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Environmental Microbiology, in the press, (2005)

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Microbiology, 151:633-637, (2005).

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Genome Comparisons5. Repeats

Microbiology, 150:3519-3521, (2004).

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Microbiology, 150:3899-3903, (2004).

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Genome Comparisons6. tRNAs and codon usage

Microbiology, 150:1603-1605, (2004).

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Genome Comparisons7. bias in codon usage

Microbiology, 150:1603-1605, (2004).

Comparative Microbial Genomics Group

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Genome Comparisons8. amino acid usage

Microbiology, 150:1603-1605, (2004).

Comparative Microbial Genomics Group

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Genome Comparisons9. Promoters

Microbiology, 150:2791-2793, (2004).

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Genome Comparisons10. Annotation quality

Trends in Genetics, 17:425-429, (2002).

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Genome Comparisons

Trends in Genetics, 17:425-429, (2002).

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Genome Comparisons

Trends in Genetics, 17:425-429, (2002).

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Trends in Genetics, 17:425-429, (2002).

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Microbiology, 150:2791-2793, (2004).

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Genome Comparisons11. Blast atlases

Microbiology, 150:3091-3093, (2004).

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BMC Genomics, 4:12, (April, 2003).

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Genome Comparisons12. Proteome comparisons

Microbiology, 151:1-4, (2005).

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Genome Comparisons13. 2-D comparisons

Microbiology, 151:333-337, (2005).

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Microbiology, 151:333-337, (2005).

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Genome Comparisons14. Secreted proteins

Microbiology, 151: in the press, (2005).

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Nature Reviews Microbiology, manuscript in preparation (2005).

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15. Transmembrane helices

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Proteobacteria

Firmicutes

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Nature Reviews Microbiology, manuscript in preparation (2005).

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Genome Comparisons15. Transmembrane helices

Nature Reviews Microbiology, manuscript in preparation (2005).

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Summary

1. I’ve listed 15 ways to compare genomes.

summary

2. Within a few years, there will be more than 1000 bacterial genomes to compare.