Computational tools and Interoperability in Comparative ... - CBS

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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1.5 1.0 0.5 0.0 T A T A A T 1 2 (a) 3 4 Position T T G A C A 1 2 (c) 3 4 Position 5 6 5 6 Bits 2.0 1.5 1.0 0.5 Bits 1 2.0 1.5 1.0 0.5 0.0 2 1 rRNA operons and promoter analysis T G A A A T T T T T T T T T G A A A A G T A 3 2 3 4 4 5 5 6 6 7 7 8 8 9 10 (b) 9 10 11 12 Position 0.0 A T T G G T Y A A A W T T T R A C C A A T Figure 3.4: Logo plots showing the initial weight matrices used for searching E. coli and Shigella genomes: –10 hexamer (a), –35 hexamer (b), UP element (c), and FIS binding motif (d). The 16S rRNA genes of all E. coli and Shigella genomes were annotated using RNAmmer. For the list of genomes, see table 3.1. All 16S rRNA genes were aligned using clustalw (Thompson et al., 1994) and a neighbor-joining tree was constructed (see figure 3.5). The figure shows additional Salmonella and Yersinia genomes for comparison. (d) 11 13 12 Position 14 13 15 16 14 17 15 18 16 19 17 20 21 18 22 19 20 21 109
Conservation of regulatory elements Escherichia coli 536 Escherichia coli APEC O1 Escherichia coli CFT073 Shigella sonnei Ss046 Shigella boydii Sb227 Shigella flexneri 2a str. 301 Shigella flexneri 2a str. 2457T Escherichia coli UTI89 Escherichia coli K12 Escherichia coli O157:H7 EDL933 Escherichia coli O157:H7 str. Sakai Escherichia coli W3110 Shigella dysenteriae Sd197 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Salmonella enterica subsp. enterica serovar Typhi Ty2 Salmonella enterica subsp. enterica serovar Typhi str. CT18 Salmonella typhimurium LT2 Yersinia pestis Antiqua Yersinia pestis CO92 Yersinia pestis KIM Yersinia pestis Nepal516 Yersinia pestis Pestoides F Yersinia pestis biovar Microtus str. 91001 Yersinia pseudotuberculosis IP 32953 Figure 3.5: Neighbor-joining tree of first 1k bases of all 16S rRNA genes of Yersinia, Salmonella, Shigella, and E. coli 110
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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
Page 82 and 83: 184 Middendorf B, Hochhut B, Leipol
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Page 108 and 109: Table 2 A selection of genes locate
Page 110 and 111: Open Access This article is distrib
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Page 114 and 115: 4314 74 Tools Abstract: Of the plet
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Page 118 and 119: 4318 74 Tools Genome atlas Intrinsi
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Page 162 and 163: Genome homology: Comparing multiple
Page 164 and 165: ing platform-‐independent Java
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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
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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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