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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B. pseudomallei 1710b, chr I 4,126,292 bp 3M 0M 1.5M 0.5M B. pseudomallei 1710b, chr II 3,181,762 bp 1.5M 1M 1M Comparative Genomics B. ambifaria AMMD 0.00 0.80 B. ambifaria MC40-6 0.00 0.80 B. cenocepacia AU 1054 0.00 0.80 B. cenocepacia HI2424 0.00 0.80 B. cenocepacia J2315 0.00 0.80 B. cenocepacia MC0-3 0.00 0.80 B. glumae BGR1 0.00 0.80 B. mallei ATCC 23344 0.00 0.80 B. mallei NCTC 10229 0.00 0.80 B. mallei NCTC 10247 0.00 0.80 B. mallei SAVP1 0.00 0.80 fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg B. multivorans ATCC 17616 fix avg 0.00 0.80 Center for Biological Sequence Analysis http://www.cbs.dtu.dk/ B. ambifaria AMMD 0.00 0.80 B. ambifaria MC40-6 0.00 0.80 B. cenocepacia AU 1054 0.00 0.80 B. cenocepacia HI2424 0.00 0.80 B. cenocepacia J2315 0.00 0.80 B. cenocepacia MC0-3 0.00 0.80 B. glumae BGR1 0.00 0.80 B. mallei ATCC 23344 0.00 0.80 B. mallei NCTC 10229 0.00 0.80 B. mallei NCTC 10247 0.00 0.80 B. mallei SAVP1 0.00 0.80 fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg B. multivorans ATCC 17616 fix avg 0.00 0.80 Center for Biological Sequence Analysis http://www.cbs.dtu.dk/ B. multivorans ATCC 17616 fix avg 0.00 0.80 B. phymatum STM815 0.00 0.80 B. phytofirmans PsJN 0.00 0.80 B. pseudomallei 1106a 0.00 0.80 B. pseudomallei 668 0.00 0.80 B. pseudomallei K96243 0.00 0.80 B. sp. 383 0.00 0.80 B. thailandensis E264 0.00 0.80 B. vietnamiensis G4 0.00 0.80 B. xenovorans LB400 0.00 0.80 W) Annotations: CDS + CDS - rRNA tRNA fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg B. multivorans ATCC 17616 fix avg 0.00 0.80 B. phymatum STM815 0.00 0.80 B. phytofirmans PsJN 0.00 0.80 B. pseudomallei 1106a 0.00 0.80 B. pseudomallei 668 0.00 0.80 B. pseudomallei K96243 0.00 0.80 B. sp. 383 0.00 0.80 B. thailandensis E264 0.00 0.80 B. vietnamiensis G4 0.00 0.80 B. xenovorans LB400 0.00 0.80 W) Annotations: Figure 2.14: Comparison of B. pseudomallei 1710b chomosome I and II against all public Burkholderia genomes. CDS + CDS - rRNA tRNA fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg fix avg Percent AT 0.21 0.42 GC Skew -0.09 0.09 Percent AT 0.21 0.42 GC Skew -0.09 0.09 21 Resolution: 1273 dev avg dev avg BLAST ATLAS Resolution: 1273 dev avg dev avg BLAST ATLAS
Genome Comparisons Bacteria fix avg 0.00 0.50 Proteobacteria fix avg 0.00 0.50 gamma fix avg 0.00 0.50 Annotations: CDS + CDS - 0M rRNA tRNA 0.5M 2.5M alpha fix avg A. borkumensis 3,120,143 bp 0.00 0.30 beta 1M 2M fix avg 0.00 0.30 1.5M delta fix avg 0.00 0.30 epsilon fix avg 0.00 0.30 Percent AT dev avg 0.40 0.51 Resolution: 1249 http://www.cbs.dtu.dk/ Center for Biological Sequence Analysis Figure 2.15: A phylome atlas of Alcanivorax borkumensis, comparing the proteome against all γ-, α-, β-, δ, and ɛ-proteobacteria available at the time of publishing. 22 Phylome ATLAS
Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
Page 4: Preface This Ph.D. thesis is writte
Page 7 and 8: thesis, the work is just being publ
Page 9 and 10: ved at blive publiceret i Standards
Page 11 and 12: viii
Page 13 and 14: Paper VI [Lagesen K, Hallin P] 1 ,
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Page 17 and 18: 3.3.3 Refining E. coli and Shigella
Page 19 and 20: xvi
Page 21 and 22: xviii 2.17 Pan- and core-genome plo
Page 24 and 25: Chapter 1 Introduction Introduction
Page 26 and 27: Chapter 2 Comparative Genomics 2.1
Page 28 and 29: Comparative Genomics the publicly a
Page 30 and 31: Comparative Genomics source CDS tot
Page 32 and 33: Comparative Genomics 1 mysql -N -B
Page 34 and 35: Listing 2.8: R code to generate a 2
Page 36 and 37: 1st U C A G U 2nd position C A G 3r
Page 38 and 39: 1st U C A G U 2nd position C A G 3r
Page 40 and 41: Escherichia coli strain K-12, subst
Page 42 and 43: Comparative Genomics
Page 46 and 47: Streptococcus Escherichia Bacillus
Page 48 and 49: 2.4 Summary Comparative Genomics Th
Page 50 and 51: Comparative Genomics 2.5 Instant in
Page 52 and 53: ‘ReSourCe is he best online submi
Page 54 and 55: up to a total of 41 different E. co
Page 56 and 57: Fig. 2 Genes (or segments) from eac
Page 58 and 59: Fig. 5 BLASTatlas of Clostridium bo
Page 60 and 61: different applications, such as ide
Page 62 and 63: 1 Comparative Genomics 2.7 Paper II
Page 64 and 65: 166 literally millions of bacterial
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Page 68 and 69: 170 resistance genes on mobile gene
Page 70 and 71: 172 involved in generating diversit
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Page 78 and 79: 180 reasons why organisms remain un
Page 80 and 81: 182 A final problem has to do with
Page 82 and 83: 184 Middendorf B, Hochhut B, Leipol
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Page 86 and 87: 2 O. N. Reva et al. Fig. 1. Genome
Page 88 and 89: 4 O. N. Reva et al. decrease of the
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10 O. N. Reva et al. encoded by a c
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12 O. N. Reva et al. systems and ef
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1 2.9 Paper IV: The origins of Vibr
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phylogenies based on alternative ho
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Figure 1 Phylogenetic tree of the 1
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25000 20000 15000 10000 5000 0 Pan
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Gap F 2M 2.5M Gap E 875k 750k 625k
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Table 2 A selection of genes locate
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Open Access This article is distrib
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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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tuB murI Fis III Fis II Fis I UP -3
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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
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RNA operons and promoter analysis O
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Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
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Code Meaning Example C Coding CCCCC
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RNA operons and promoter analysis 3
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P2 -10 -35 UP P1 -10 -35 UP FIS FIS
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1 rRNA operons and promoter analysi
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Using HMMs also simplifies the use
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Information content Information con
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of the annotation. Some of the majo
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where match states stop around 10 c
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1 rRNA operons and promoter analysi
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synthesis in flow cells to simultan
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Read absence. A boolean where ‘on
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Hallin, et al. Figure 4 | The dataf
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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Chapter 5 Conclusion and perspectiv
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Appendix A Appendix: Workshops, tea
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Appendix B Appendix: Ph.D. study pl
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Danmarks Tekniske Universitet AFI,
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Danmarks Tekniske Universitet AFI,
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Appendix C Appendix: Courses C.1 Gl
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D.2 Sample output from queryGenomes
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Appendix: Software 13 w a r n " $ o
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Appendix: Software 109 m y ( $ m i
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Appendix: Software 25 [ ] A l t e r
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BIBLIOGRAPHY J. Rogers, P. F. Stadl
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BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
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BIBLIOGRAPHY Velicer, F.-J. Vorholt
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