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tuB murI Fis III Fis II Fis I UP -35 -10 min: -4nt center:2nt max:4nt min: 0nt center:3nt max:6nt min: 13nt center:16nt max:19nt P1 rRNA operons and promoter analysis 16S tRNA 23S 5S Glu murB -35 -10 min: 0nt center:3nt max:6nt P2 P1 min: 13nt center:16nt max:19nt Figure 3.2: The promotor structure of the rrnB operon in E. coli. -35 ! -10 ! -10 -35 Figure 3.3: The –10 and –35 hexamers of the E. coli σ 70 promotor correspond to the motifs being located on opposite side of the DNA helix. Delition or insertions of the spacing cases a shift of approx. 36deg per nucleotide. 107
Conservation of regulatory elements values. nb,p Rb,p = log2(4) + log2 N L Rtot = RB,p p=1 (3.1) –where b ∈ AT GC iterates through the four bases, p denotes the position in the alignment, L is the length of the alignment (or width of the matrix), and nb,p is the number of bases b at position p, and B denotes the nucleotide at position p in the query sequence. Shultzaberger and co-workers account for the helical facing by introducing the accessibility, n(d) (equation 3.2) and the gap surprisal, GS(d) (see equation 3.3). n(d) = 1 + cos[ 2π (d − c)] (3.2) w –where c is the center distance between two binding sites (e.g. optimally spaced), d is the query distance, w = 10.6 is the distance of a one helix turn of B-form DNA. Finally, this gives GS(d) as follows: n(d) GS(d) = log2 N (3.3) –where N is the sum of all n(d) (see equation 3.4). The sign of the GS(d) was changed from the original equation described by Shultzaberger and co-workers to allow for combining all scores by addition. N = max d=min n(d) (3.4) –where min and max are the boundaries of a given window examined. Finally, summarizing all Ri and GS(d) values gives the total information of all motifs and all spacers (see figure 3.5) Ri(tot) = Ri(m1) + GS(d, m1) + Ri(m2) + ... + GS(d, mn−1) + Ri(mn) (3.5) 3.3.1 Modeling the P1 and P2 in selected enterics Existing experimentally verified –10 and –35 hexamers (Huerta & Collado-Vides, 2003) were converted into Rb,p matrices together with data for known UP elements (Estrem et al., 1998) and FIS binding sites (Hengen et al., 1997). Figure 3.4 shows logo plots of the information content of these studies. The initial weight matrices founded the basis for iteratively building the final information model of the P1 and P2 promotor structure, using the following procedure: 1. E. coli and Shigella genomes 108 2. rRNA gene finding and make upstream sequence 3. Apply models based on literature weight matrices 4. Refine weight matrices according to observations 5. Formulate final model
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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
Page 80 and 81: 182 A final problem has to do with
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Page 108 and 109: Table 2 A selection of genes locate
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Page 114 and 115: 4314 74 Tools Abstract: Of the plet
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Page 138 and 139: Code Meaning Example C Coding CCCCC
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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
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Page 178 and 179: 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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