comparative microbial genomics group center for biological sequence analysis the technical...
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Methods to Compare Microbial Genomes
20 Methods to Compare Microbial Genomes
Dave UsseryBiological Sequence AnalysisDTU course # 2780327 April, 2007
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rRNA tree
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2. Number genes [coding density]
3. AT content
6. Repeats
4. Oligomer skews
5. Chromosome alignment
8. tRNAs and codon usage
9. Bias in codon usage
10. Amino acid usage
1. Length
7. Periodicity
Gen
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20 Methods to Compare Bacterial Genomes
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14. Proteome comparisons
13. Blast atlases
12. Annotation quality
15. 2-D correlation of properties
16. Sigma Factors
17. Two-component systems
18. Transcription Factors
19. Membrane Proteins
20. Secreted Proteins
11. Promoters
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Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).
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Comparative Microbial Genomics groupC
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What have we learned from 300 sequenced bacterial genomes?
1. Genetic diversity is greater than we thought.
4. Generally G’s are biased towards the leading strand, but the strand bias of A’s is tax-specific.
2. Very large genomes tend to be GC-rich, whilst small genomes tend to be AT-rich.
3. There are patterns, both locally and globally of AT-richness in bacterial chromosomes.
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Comparative Microbial Genomics groupC
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1. Length
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Comparative Microbial Genomics groupC
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Friis, Jensen, and Ussery
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Bioinformatics, 20:3682-3686, (2004).
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Microbiology, 150:749-752, (2004).
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Microbiology, 150:749-752, (2004).
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tRNAs and codon usage
Microbiology, 150:1603-1605,
(2004).
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Clavibacter michiganensis27% A+T content
Nitrococcus oceani50% A+T content
Wigglesworthia glossinidia78% A+T content
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Soil Bacteria
Gram +Mollicutes Enterics
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amino acid usage
Microbiology, 150:1603-1605,
(2004).
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Bioinformatics, 20:3682-3686, (2004).
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Peder Worning and Lars Juhl Jensen et al., Environmental Microbiology, 8:353-361 (Feb. 2006)
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Peder Worning and Lars Juhl Jensen et al., Environmental Microbiology, 8:353-361 (Feb. 2006)
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P1
P2
P3
P4
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16. Sigma Factors
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Vibrios
Gamma-Proteobacteria
Alpha, Beta, Delta, Epsilon-Proteobacteria
Firmicutes
Chlamydia
Spirochaetes
Actinobacteria
Bacteriodes
σ54
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# ECF Sigma Factors in 250 Bacterial Genomes
Microbiology, 151:3147-3151, (2005).
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20. Secreted proteins
Vibrio
Microbiology, 151:1013-1017,
(2005).
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Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).
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