Computational tools and Interoperability in Comparative ... - CBS

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1st U C A G U 2nd position C A G 3rd 19 Phe 4 Ser 14 Tyr 3 Cys U 19 Phe 11 Ser 13 Tyr 8 Cys C 6 Leu 4 Ser 2 Stop 1 Stop A 7 Leu 12 Ser 0 Stop 16 Trp G 8 Leu 5 Pro 12 His 13 Arg U 16 Leu 8 Pro 11 His 31 Arg C 3 Leu 4 Pro 7 Gln 3 Arg A 72 Leu 30 Pro 38 Gln 10 Arg G 20 Ile 5 Thr 12 Asn 4 Ser U 33 Ile 31 Thr 22 Asn 22 Ser C 3 Ile 3 Thr 24 Lys 2 Arg A 27 Met 13 Thr 13 Lys 1 Arg G 10 Val 10 Ala 26 Asp 13 Gly U 21 Val 44 Ala 24 Asp 43 Gly C 7 Val 8 Ala 27 Glu 6 Gly A 33 Val 43 Ala 27 Glu 14 Gly G Comparative Genomics Table 2.3: Codon usage in Klebsiella pneumoniae NTUH-K2044. Frequencies are measured per thousand. A total of 4,697,097 base pairs are examined in 5,006 ORFs. Z−score −2.0 −1.5 −1.0 −0.5 0.0 Buchnera_aphidicola_Cc: AT content −400 −200 0 200 400 Distance from translation start Figure 2.7: AT content profile 400 bp upstream and downstram of annotated translation starts in Buchnera aphidicola Cc. 15
Genome Comparisons Figure 2.8: Deamination of cytosine (C) into uracil (U) 2.3.5 Base composition and DNA repair Klebsiella is often found in plant products, root surfaces and living trees, fresh vegetables, and foods with high content of sugars and acids, such as frozen orange juice concentrate. Klebsiella pneumoniae can causes urinary tract infections and the NTUH-K2044 strain was isolated from a patient with liver abscess and meningitis. The broad range of ecological niches in which Klebsiella lives share the property of being rich in energy and nitrogen. Nitrogen-fixing aerobic bacteria are known to have higher chromosomal GC content (McEwan et al., 1998), explained by the nitrogen requirement to replicate the chromosome; an AT base pairs contains 7 nitrogen atoms whereas a GC pair contains 8 nitrogen atoms. Cytosine pairs are prone to mutation caused by spontaneous deamination into uracil (Visnes et al., 2009) (figure 2.8). In E. coli the two enzymes uracil N -glycosylase and apurinic (AP) endonuclease are responsible for the repair of this mutation. However, in Buchnera aphidicola Cc, which is a small reduced genome, these two enzymes are absent (confirmed by protein BLAST). A negative selection is likely to occur in organisms with high chromosomal GC content and the lack of a functional repair mechanism. Hence, base composition of the bacterial genome is by no means random and adjusting the overall GC contant through evolution may be yet another way to adapt to the environment. 2.3.6 BLASTmatrix - proteome comparison The BLASTmatrix tool allows for visualization of proteome similarity between larger numbers of organisms. For each of the pairwise combinations of proteomes, a BLAST is performed. Two proteins are declared homologous when 50% of the protein is aligned and 50% of the residues within the alignment are conserved. For a report of proteome A against proteome B, all homologous proteins are then grouped into families and the similarity between A and B is calculated as the number of families having both organism A and B represented. The BLAST report is cached, based on MD5 checksums of the proteomes. This enables the tool to efficiently reuse previous results, when organisms are added to a comparison. This is repeated for all N j=1 j combinations and for each combination a square is drawn containing the following information: the similarity as percentage of all families of A and B, the number of shared families and the total number of families. A small example matrix is shown in figure 2.9. The percentage is used to color-code the square to allow for easier overview of larger comparisons. The software requires a configuration in XML as first argument. In appendix D.4 a Perl script is provided which automatically constructs a configuration that compares all published Campylobacter proteomes, by querying the Genome Atlas Database. The output of the BLASTmatrix configuration is shown in figure 2.10. The software has been used in different publications (Binnewies et al., 2005, 2006) and has been updated a number of times since. The older versions contained both BLAST directions and showed the number of shared proteins, leaving the diagram redundant. The recent version avoids this by instead plotting the shared families which renders the plot symmetrical across the diagonal. This allows the lower triangle to be removed. 16
Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
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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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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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RNA operons and promoter analysis O
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Code Meaning Example C Coding CCCCC
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1 rRNA operons and promoter analysi
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Using HMMs also simplifies the use
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of the annotation. Some of the majo
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where match states stop around 10 c
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1 rRNA operons and promoter analysi
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synthesis in flow cells to simultan
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Read absence. A boolean where ‘on
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Hallin, et al. Figure 4 | The dataf
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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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