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1 Comparative Genomics 2.10 Paper V: Tools for comparison of bacterial genomes
74 Tools for Comparison of Bacterial Genomes T. M. Wassenaar 1,2 . T. T. Binnewies 1,3 . P. F. Hallin 1 . D. W. Ussery 1, * 1 Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark *dave@cbs.dtv.dk 2 Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany 3 Roche Diagnostics Ltd., Advanced Systems Group, Global Platforms & Support, Rotkreuz, Switzerland 1 Introduction . . . . . . ..................................................................4314 2 Genomic DNA Sequence Comparisons . ...........................................4314 3 Visualization of Genomic Data: The Genome Atlas ..............................4317 4 Whole Genome Alignment Methods . . . . ...........................................4319 5 Comparing the Coding Fraction of Genomes . . . . . . . . ..............................4321 6 Codon Usage Comparisons . . . . .....................................................4322 7 Protein Sequence Comparisons . . . . . . . . . ...........................................4322 8 Gene Synteny and Genome Islands . . . . . ...........................................4325 9 Minimal Information About a Genome Sequence . . . ..............................4325 10 Research Needs . . . ..................................................................4325 K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_337, # Springer-Verlag Berlin Heidelberg, 2010
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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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Page 64 and 65: 166 literally millions of bacterial
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Page 78 and 79: 180 reasons why organisms remain un
Page 80 and 81: 182 A final problem has to do with
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Page 86 and 87: 2 O. N. Reva et al. Fig. 1. Genome
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Page 100 and 101: phylogenies based on alternative ho
Page 102 and 103: Figure 1 Phylogenetic tree of the 1
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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 126 and 127: 4326 74 Tools information, as genet
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Page 134 and 135: RNA operons and promoter analysis O
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Page 138 and 139: Code Meaning Example C Coding CCCCC
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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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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