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Genome homology: Comparing multiple Burkholderia species A comparative study aimed at mapping for exam-‐ ple pathogenic islands or gene losses among dif-‐ ferent bacterial genomes can benefit from a graph-‐ ical representation provided by the BLASTatlas method. The genus of Burkholderia covers a num-‐ ber of important animal and human pathogens known to cause melioidosis (B. pseudomallei) and pulmonary infection in cystic fibrosis (CF) patients (B. cepacia), whereas B. thailandensis, which is closely related to B. pseudomallei, rarely gives rise to diseases in humans [29,30]. Both species of B. thailandensis and B. mallei display large chromo-‐ somal deletions when compared to B. pseudomallei. However, the more scattered nature of the Hallin, et al. gene loss observed in B. thailandensis suggests that B. mallei evolved from B. pseudomallei through the loss of larger regions [31]. These dele-‐ tions are evident from the atlas shown in Figure 6 where the two chromosomes of Burkholderia pseudomallei 1710b are used as BLASTatlas refer-‐ ence in a comparison with 14 publicly available Burkholderia genomes (B. thailandensis plus all species having two or more strains sequenced, see supplemental data). In addition it is evident that a strong preference of deletion exist for chromo-‐ some II. Ong and co-‐workers report that deletions in chromosome II counts for 70% and 61% of the total gene loss in B. mallei and B. thailandensis, respectively. Figure 6 | BLASTatlas of Burkholderia pseudomallei 1710b chromosomes I+II compared with 14 Burkholderia species. Showing from the outermost circles: B. ambifaria (2, purple), B. cenocepacia (4, red) B. thailandensis (1, green) 10774, B. mallei (4, green), and B. pseudomallei (3, blue). Innermost circles show percent AT, and CG skew. Note, that to allow visual comparison between B. thailandensis and B. mallei, both species are colored green: the outermost green lane corresponds to the single B. thailandensis, whereas the remaining four green lanes are all B. mallei. GenBank accession numbers as well as interactive plots are available through the supplemental data section. http://standardsingenomics.org 211
GeneWiz browser The SIDD atlas: Annotation of regulatory elements The browser application enables the user to ap-‐ pend various annotation marks such as transcrip-‐ tion start site arrows, gene labels, and boxes. A final example illustrates how these marks can be used to integrate known regulatory elements with DNA properties and gene annotations to draw a more complete picture of a promoter region. The regulatory elements of the E. coli K12 MG1665 rrn operons [32] have been annotated in a standard SIDD atlas, providing a visualization of the P1/P2 promoter structure (Figure 7). A zoom of the pro-‐ moter region reveals a strong SIDD site near the predominant P1 promoter approximately 40 bp. upstream of the P1 transcription start site. The transcription factor FIS stimulates transcription at several promoters, and for example the binding of FIS at the leuV promoter [33] has been suggested to transmit the superhelical destabilization down-‐ stream to the point where the RNAP twists and opens the helix [34]. This model may be valid for the rrnB P1 promoter also, as the activity of leuV and rrnB P1 are comparable [35]. Figure 7 | A zoom upstream of the E. coli K12 MG1665 rrnB operon. The three outer-most lanes show SIDD at three superhelix densities of sigma=-0.055, -0.045, and -0.035. The lower free energy required to melt the helix can be observed near the UP element of P1, for the SIDD lane at sigma = -0.045. The atlas is available for zooming on the supplemental data section. Discussion Visualization of the multidimensional information that is represented by a single genome sequence remains complex. An indispensable property of a genome visualization tool is that it must be zoom-‐ able, so that information can be interpreted at varying scales. Two recently published methods, the DNAPlotter [36] and the Genome Projector [37], both enable the user to build circular plots of numerical data related to genes as well as graphs of numerical data pertaining to the nucleotides. These tools create static graphics and allows only for proportional zooming, hence making the plot hard to interpret when zooming too deep. Both of these tools allow for visualization of individual genomes, but do not allow easy comparison across multiple genomes. With the ease of new genome sequences becoming available, it is essential to be able to quickly compare other genomes to a refer-‐ ence. A number of other tools approach genome visuali-‐ zation from different angles: Genome Diagram [38] and Circos [39] are command line programs gene-‐ rating publication quality static images and vector graphics. Although these tools allow comparison of other genomes, are flexible and allow visualiza-‐ tion of numerical data, they lack an interactive layer. The GeneWiz browser described here uses dis-‐ proportional zooming to overcome this. From a technical perspective, the choice of programming language for writing graphical browsers is of im-‐ portance. There are obvious advantages of provid-‐ 212 Standards in Genomic Sciences
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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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3.3.3 Refining E. coli and Shigella
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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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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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Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
Page 190 and 191: D.2 Sample output from queryGenomes
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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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