Computational tools and Interoperability in Comparative ... - CBS

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C Appendix: Courses 165 C.1 Global regulatory networks in microorganisms . . . . . . . . . . . . . . . . . 165 C.2 Protein Structure and Computational Biology . . . . . . . . . . . . . . . . . 165 C.3 Biological Sequence Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 165 C.4 Comparative Genome Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 165 C.5 Doctorial seminar on business economics for academic entrepreneurs . . . . 165 C.6 ECTS summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 D Appendix: Software 166 D.1 fetchgbk manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166 D.2 Sample output from queryGenomes . . . . . . . . . . . . . . . . . . . . . . . 167 D.3 BLASTatlas configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 D.3.1 file blast.cfg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 D.3.2 file custom.cfg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 D.4 BLASTmatrix example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 D.5 iscan source code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 D.6 quasi mktemp manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Bibliography 174 xv
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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
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Page 13 and 14: Paper VI [Lagesen K, Hallin P] 1 ,
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Page 17: 3.3.3 Refining E. coli and Shigella
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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
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Page 48 and 49: 2.4 Summary Comparative Genomics Th
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170 resistance genes on mobile gene
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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176 Fig. 5 Genome length distributi
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178
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180 reasons why organisms remain un
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182 A final problem has to do with
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184 Middendorf B, Hochhut B, Leipol
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1 Comparative Genomics 2.8 Paper II
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2 O. N. Reva et al. Fig. 1. Genome
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4 O. N. Reva et al. decrease of the
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6 O. N. Reva et al. of which are kn
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8 O. N. Reva et al. compiled into a
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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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