C e n t e r f o r B i o l o g i c a l S e q u e n c e A n a l y s i s T h e T e c h n i c a l U n i v e r s i t y o f D e n m a r k D T U Comparative Microbial Genomics Dave Ussery Biological Sequence Analysis DTU course # 27803 15 April, 2005
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Cen
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics
Dave UsseryBiological Sequence AnalysisDTU course # 2780315 April, 2005
Cen
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Cen
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Outline
• Introduction• Genome (DNA properties)• Transcriptome (RNA properties)• Proteome comparisons
15 methods (!)
Cen
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r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
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of D
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mark D
TU
Bacteria are very small!
Tim
TineMette
Bjørn
Kristoffer Anne
Peter
Heng
Natasja
Hanni
Lars
Lise
Nikolaj Tom
Cen
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log
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eq
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e T
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of D
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TU
Warning - you’ve already seen some of this before!
Cen
ter fo
r Bio
log
ical S
eq
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ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
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mark D
TU
rRNA tree
Cen
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Comparative Microbial Genomics Group
Biological info.?
Genome Comparisons
1. Chromosome alignment
Cen
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Microbiology, 150:2491-
2493, (2004).
Cen
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Microbiology, 150:513-515, (2004).
Cen
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Genome Comparisons
3. AT content
Microbiology, 150:749-751, (2004).
Cen
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3. AT content
Bioinformatics, 20:3682-3686, (2004).
Cen
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Cen
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r Bio
log
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eq
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ce A
naly
sis Th
e T
ech
nica
l Un
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of D
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mark D
TU
Cen
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l Un
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3. AT content - globally
Microbiology, 150:749-752, (2004).
Cen
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l Un
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of D
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3. AT content - locally
Microbiology, 150:749-752, (2004).
Cen
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sis Th
e T
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nica
l Un
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of D
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TU
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).
Cen
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Genome Comparisons6. tRNAs and codon usage
Microbiology, 150:1603-1605, (2004).
Cen
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Cen
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naly
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e T
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nica
l Un
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of D
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TU
Genome Comparisons7. bias in codon usage
Microbiology, 150:1603-1605, (2004).
Comparative Microbial Genomics Group
Cen
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Cen
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nica
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of D
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Genome Comparisons8. amino acid usage
Microbiology, 150:1603-1605, (2004).
Comparative Microbial Genomics Group
Cen
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Cen
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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).
Cen
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of D
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Genome Comparisons
Trends in Genetics, 17:425-429, (2002).
Cen
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of D
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TU
Trends in Genetics, 17:425-429, (2002).
Cen
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r Bio
log
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eq
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sis Th
e T
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nica
l Un
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of D
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TU
Microbiology, 150:2791-2793, (2004).
Cen
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r Bio
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l Un
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of D
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TU
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).
Cen
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sis Th
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nica
l Un
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of D
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TU
Cen
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Cen
ter fo
r Bio
log
ical S
eq
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ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
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mark D
TU
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.
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