Computational tools and Interoperability in Comparative ... - CBS

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2.4 Summary Comparative Genomics This chapter presents a number of comparative genomics and visualization tools used in a genome annotation and analysis pipeline. Visualization methods have been shown to help draw biological conclusions about adaptation to environmental niches, pathogenic properties, and comparison of many other genomic properties including proteome similarity. Overviewing the large amount of genomic data constitutes a constant challenge that will need more attention in the future as sequencing technology becomes more and more common. How can one visualize comparison of a thousand genomes? Soon there will be a need to compare sets of thousands of genomes. 25
Summary 26
Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
Page 4: Preface This Ph.D. thesis is writte
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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
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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
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Page 40 and 41: Escherichia coli strain K-12, subst
Page 42 and 43: Comparative Genomics
Page 44 and 45: 3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
Page 46 and 47: Streptococcus Escherichia Bacillus
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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
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Page 64 and 65: 166 literally millions of bacterial
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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
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Page 94 and 95: 10 O. N. Reva et al. encoded by a c
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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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