Computational tools and Interoperability in Comparative ... - CBS

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RNA operons and promoter analysis Organism Accession Reference Escherichia coli 101-1 AAMK00000000 (unpublished) Escherichia coli 53638 AAKB00000000 (unpublished) Escherichia coli 536 CP000247 (Brzuszkiewicz et al., 2006) Escherichia coli APEC O1 CP000468 (Johnson et al., 2007) Escherichia coli B171 AAJX00000000 (unpublished) Escherichia coli B7A AAJT00000000 (unpublished) Escherichia coli B AAWW00000000 (unpublished) Escherichia coli CFT073 AE014075 (Welch et al., 2002) Escherichia coli E110019 AAJW00000000 (unpublished) Escherichia coli E22 AAJV00000000 (unpublished) Escherichia coli F11 AAJU00000000 (unpublished) Escherichia coli K12 U00096 (Blattner et al., 1997) Escherichia coli O157:H7 EDL933 AE005174 (Perna et al., 2001) Escherichia coli O157:H7 str. Sakai BA000007 (Hayashi et al., 2001) Escherichia coli SECEC SMS-3-5 ABAQ00000000 (unpublished) Escherichia coli UTI89 CP000243 (Chen et al., 2006) Escherichia coli W3110 AP009048 (Hayashi et al., 2006) Shigella boydii CDC 3083-94 AAKA00000000 (unpublished) Shigella boydii Sb227 CP000036 (Yang et al., 2005) Shigella dysenteriae 1012 AAMJ00000000 (unpublished) Shigella dysenteriae Sd197 CP000034 (Yang et al., 2005) Shigella flexneri 2a str. 2457T AE014073 (Liao et al., 2003) Shigella flexneri 2a str. 301 AE005674 (Jin et al., 2002) Shigella sonnei Ss046 CP000038 (Yang et al., 2005) Table 3.1: Escherichia coli and Shigella genomes currently available at the time of the work (October 2007) 111
Conservation of regulatory elements Ri Ri −15 −10 −5 0 5 10 −10 −5 0 5 10 15 P1: Raw combined scores, −10,−35, UP (E.coli) (N=63) −500 −400 −300 −200 −100 0 Position relative to 16S gene start (a) P2: Raw combined scores, −10,−35, UP (E. coli) (N=63) −500 −400 −300 −200 −100 0 Position relative to 16S gene start (c) Ri Ri −15 −10 −5 0 5 10 15 −10 −5 0 5 10 15 P1: Adjusted combined scores, −10,−35, UP (E.coli) (N=63) −500 −400 −300 −200 −100 0 Position relative to gene start (b) P2: Adjusted combined scores, −10,−35, UP (E. coli) (N=63) −500 −400 −300 −200 −100 0 Position relative to gene start Figure 3.6: Profiles showing the maximum Ri(tot) scores of the initial weight matrices applied to E. coli and Shigella: Unadjusted P1 scores (a), Adjusted P1 scores (b), Unadjusted P2 scores (c), and Adjusted P2 scores (d) 3.3.2 Iterating weight matrix frequencies The program iscan was developed to query a given DNA sequence and for every position in this sequence calculate the maximum Ri(tot) that can be obtained by trying out different spacing configuraitons within a specified window. The iscan algorithm aligns the first matrix with the query (in this case the –10 hexamer) and tries all distances between 13 and 19 nucleotides towards the –35 hexamer, using 16 nucleotides as the center. Then the program locks the optimal of those distances, and continues with the next box (in this case the the UP element) until all elements have been included. For source code, see appendix D.5. The spacing configuration of the two models is shown in figure ??. The maximum Ri(tot) values of all operons were stacked and average and standard deviation values were plotted as function of position. Because the distance between P1/P2 and the 16S gene varies slightly, the unadjusted plots appear noisy. By shifting the plots slightly by aligning to local maxima around P1 and P2 renders the P1 and P2 model scores sharper (see figure 3.6). 3.3.3 Refining E. coli and Shigella models All peaks of Ri(tot) around the regions of P1 and P2 have been collected, and the P1 and P2 models were refined by adjusting matrix parameters according to the observed base frequencies in the hits obtained. The logo plots of are shown in figure 3.7 112 (d)
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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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Page 114 and 115: 4314 74 Tools Abstract: Of the plet
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Page 130 and 131: tuB murI Fis III Fis II Fis I UP -3
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Page 136 and 137: Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
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Page 164 and 165: ing platform-‐independent Java
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Page 178 and 179: Chapter 5 Conclusion and perspectiv
Page 180 and 181: Appendix A Appendix: Workshops, tea
Page 182 and 183: 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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