Computational tools and Interoperability in Comparative ... - CBS

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Appendix B Appendix: Ph.D. study plan Appendix: Ph.D. study plan 159
Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse September 2005 Nedenstående studieplan er accepteret af studerende og vejleder Hovedvejleders underskrift lokal nr. Studerendes underskrift Ph.d.-studieplan Ph.d.-studerendes navn: Peter Fischer Hallin Cpr.-nr.: 160877 2053 Ph.d.-program: Bioinformatics Institut: BioCentrum Startdato: March 1 2006 Slutdato: February 2009 Hovedvejleder: Associate professor David W. Ussery (Titel, navn, institut, tlf.) BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Lyngby, Denmark E-mail address: dave@cbs.dtu.dk Phone (direct): (+45) 45 25 24 88 Medvejleder: Guest Researcher Gertrude Maria Wassenaar (Titel, navn, institution/virksomhed) BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Lyngby, Denmark E-mail address: trudy@cbs.dtu.dk Phone (direct): (+45) 45 25 24 77 Dato: 18-11-2007 Studiets titel: DNA Structural Analysis and Transcript Prediction in Prokaryotic genomes 1
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Peter Fischer Hallin | 2009 Peter F
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Preface This Ph.D. thesis is writte
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thesis, the work is just being publ
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ved at blive publiceret i Standards
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viii
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Paper VI [Lagesen K, Hallin P] 1 ,
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xii
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3.3.3 Refining E. coli and Shigella
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xvi
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xviii 2.17 Pan- and core-genome plo
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Chapter 1 Introduction Introduction
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Chapter 2 Comparative Genomics 2.1
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Comparative Genomics the publicly a
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Comparative Genomics source CDS tot
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Comparative Genomics 1 mysql -N -B
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Listing 2.8: R code to generate a 2
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1st U C A G U 2nd position C A G 3r
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1st U C A G U 2nd position C A G 3r
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Escherichia coli strain K-12, subst
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Comparative Genomics
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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
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Streptococcus Escherichia Bacillus
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2.4 Summary Comparative Genomics Th
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Comparative Genomics 2.5 Instant in
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‘ReSourCe is he best online submi
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up to a total of 41 different E. co
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Fig. 2 Genes (or segments) from eac
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Fig. 5 BLASTatlas of Clostridium bo
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different applications, such as ide
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1 Comparative Genomics 2.7 Paper II
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166 literally millions of bacterial
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168
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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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Page 134 and 135: RNA operons and promoter analysis O
Page 136 and 137: Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
Page 138 and 139: Code Meaning Example C Coding CCCCC
Page 140 and 141: RNA operons and promoter analysis 3
Page 142 and 143: P2 -10 -35 UP P1 -10 -35 UP FIS FIS
Page 144 and 145: 1 rRNA operons and promoter analysi
Page 146 and 147: Using HMMs also simplifies the use
Page 148 and 149: Information content Information con
Page 150 and 151: of the annotation. Some of the majo
Page 152 and 153: where match states stop around 10 c
Page 154 and 155: 1 rRNA operons and promoter analysi
Page 156 and 157: synthesis in flow cells to simultan
Page 158 and 159: Read absence. A boolean where ‘on
Page 160 and 161: Hallin, et al. Figure 4 | The dataf
Page 162 and 163: Genome homology: Comparing multiple
Page 164 and 165: ing platform-‐independent Java
Page 166 and 167: 34. Wang H, Noordewier M, Benham CJ
Page 168 and 169: Chapter 4 Web Services and Interope
Page 170 and 171: Web Services and Interoperability i
Page 178 and 179: Chapter 5 Conclusion and perspectiv
Page 180 and 181: Appendix A Appendix: Workshops, tea
Page 184 and 185: Danmarks Tekniske Universitet AFI,
Page 186 and 187: Danmarks Tekniske Universitet AFI,
Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
Page 190 and 191: D.2 Sample output from queryGenomes
Page 192 and 193: Appendix: Software 13 w a r n " $ o
Page 194 and 195: Appendix: Software 109 m y ( $ m i
Page 196 and 197: Appendix: Software 25 [ ] A l t e r
Page 198 and 199: BIBLIOGRAPHY J. Rogers, P. F. Stadl
Page 200 and 201: BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
Page 202 and 203: BIBLIOGRAPHY Velicer, F.-J. Vorholt
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