Computational tools and Interoperability in Comparative ... - CBS

More documents

Recommendations

Info

4 O. N. Reva et al. decrease of the base stacking energy. Figure 4 visualizes the phylogenetic relationships differentiated by TU patterns of 29 g-Proteobacterial taxa each of which represented by not more than a single sequenced strain. A. borkumensis forms a cluster with Pseudomonas, Methylococcus, Xanthomonas and Xylella (Fig. 4). Despite the variation in GC-content, from 52 to 54% in Xylella and Alcanivorax to more than 65% in Xanthomonas and Pseudomonas, the TU patterns of these Fig. 3. Tetranucleotide usage patterns of A. borkumensis SK2, P. putida KT2440, E. coli K12 MG1655 and S. oneidensis MR-1. The deviation Dw of observed from expected counts is shown for all 256 tetranucleotide words (16 ¥ 16 cells) by colour code (right bar). Tetranucleotides are grouped into 39 classes of equivalent structural features (Baldi and Baisnee, 2000) and sorted by decreasing base stacking energy row-by-row starting at the upper left corner (class 39). The words corresponding to the cells in colour plots are shown in the table in lower part of the figure. microorganisms are similar and separated from other g-Proteobacteria. There is an abundance of GC-rich tetranucleotides with high base stacking energy in the sequence of A. borkumensis SK2 (words belonging to equivalence classes 37–39, 30 and 27) that is similar to the TU pattern of P. putida KT2440 (Fig. 3). Words of the AT-rich classes 7, 10, 13 and 32 are significantly underrepresented in both species. The major difference between TU patterns is the abundance of poly A and poly ©2007TheAuthors Journal compilation © 2007 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology
T stretches (words of class 1) in A. borkumensis in correspondence with its lower GC-content of 54.7%. Although E. coli and S. oneidensis share a similar GC contents with A. borkumensis, their tetranucleotides usage is different from Alcanivorax. The parity of GC with AT in the genome correlates with a balanced use of GC-rich and AT-rich words with high and low base stacking energy. In contrast, words with intermediate values of the base stacking energy (classes 25, 31, 36 and 29) are mostly underrepresented (Fig. 3). The data suggests that oligonucleotide usage drives GC-content and not vice versa. To give another example: the GC-rich words of class 21 are rare in all g-Proteobacteria irrespectively of their GC-content (Fig. 3), but these words are overrepresented in a-Proteobacteria (Agrobacterium, Bordetella, Caulobacter, Rhizobium). Anomalous local TU patterns in the A. borkumensis genome A. borkumensis shares a common taxonomic group with Pseudomonas, Methylococcus, Xanthomonas and Xylella. Although the TU patterns are genome specific signatures, the oligonucleotide usage may vary locally in segments made up by horizontally acquired elements, phylogenetically ancient genes such as rRNAs or genes Comparative genomics of Alcanivorax borkumensis 5 Fig. 4. Tree of the similarity of TU patterns of completely sequenced g-Proteobacteria strains. Distance D-values (see Experimental procedures) between two TU patterns were calculated, and the tree was constructed from the distance matrix of all D-values by the minimum evolution neighbour-joining method (Saitou and Nei, 1987). with peculiar codon usage (Reva and Tümmler, 2004; 2005). In other words, anomalous local TU patterns can be expected for the most recent and the most ancient genes. Local TU patterns were calculated in 8 kbp long overlapping sliding windows in steps of 2 kbp. Distances D between local and global TU patterns are shown in Fig. 5. The 18 regions with D-values above the 95% confidence interval are listed in Table 1. Three clusters with anomalous D-values encode ribosomal RNAs that belong to the most ancient and conserved elements of all bacterial genomes. All the other 15 regions with atypical TU most likely were recently acquired, three of which contain transposase genes. In total 11 transposases were annotated in the A. borkumensis SK2 genome but for five of them no significant deviations of the local TU patterns were detected in adjacent regions. If inserted mobile elements had lost their mobility due to disruptive mutations, they undergo an amelioration process smoothing the differences in oligonucleotide usage between inserts and the host genome and thus cannot be detected by anomalous TU patterns anymore (Pride et al., 2003). Five regions with high D-values (Fig. 5) only encode hypothetical proteins (Table 1). One further region contains genes of the type II secretion system and two regions encode type IV pili biogenesis proteins the latter ©2007TheAuthors Journal compilation © 2007 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology
Page 1 and 2:
Peter Fischer Hallin | 2009 Peter F
Page 4:
Preface This Ph.D. thesis is writte
Page 7 and 8:
thesis, the work is just being publ
Page 9 and 10:
ved at blive publiceret i Standards
Page 11 and 12:
viii
Page 13 and 14:
Paper VI [Lagesen K, Hallin P] 1 ,
Page 15 and 16:
xii
Page 17 and 18:
3.3.3 Refining E. coli and Shigella
Page 19 and 20:
xvi
Page 21 and 22:
xviii 2.17 Pan- and core-genome plo
Page 24 and 25:
Chapter 1 Introduction Introduction
Page 26 and 27:
Chapter 2 Comparative Genomics 2.1
Page 28 and 29:
Comparative Genomics the publicly a
Page 30 and 31:
Comparative Genomics source CDS tot
Page 32 and 33:
Comparative Genomics 1 mysql -N -B
Page 34 and 35:
Listing 2.8: R code to generate a 2
Page 36 and 37:
1st U C A G U 2nd position C A G 3r
Page 38 and 39: 1st U C A G U 2nd position C A G 3r
Page 40 and 41: Escherichia coli strain K-12, subst
Page 42 and 43: Comparative Genomics
Page 44 and 45: 3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
Page 46 and 47: Streptococcus Escherichia Bacillus
Page 48 and 49: 2.4 Summary Comparative Genomics Th
Page 50 and 51: Comparative Genomics 2.5 Instant in
Page 52 and 53: ‘ReSourCe is he best online submi
Page 54 and 55: up to a total of 41 different E. co
Page 56 and 57: Fig. 2 Genes (or segments) from eac
Page 58 and 59: Fig. 5 BLASTatlas of Clostridium bo
Page 60 and 61: different applications, such as ide
Page 62 and 63: 1 Comparative Genomics 2.7 Paper II
Page 64 and 65: 166 literally millions of bacterial
Page 66 and 67: 168
Page 68 and 69: 170 resistance genes on mobile gene
Page 70 and 71: 172 involved in generating diversit
Page 72 and 73: 174 recipient DNA. A feature observ
Page 74 and 75: 176 Fig. 5 Genome length distributi
Page 76 and 77: 178
Page 78 and 79: 180 reasons why organisms remain un
Page 80 and 81: 182 A final problem has to do with
Page 82 and 83: 184 Middendorf B, Hochhut B, Leipol
Page 84 and 85: 1 Comparative Genomics 2.8 Paper II
Page 86 and 87: 2 O. N. Reva et al. Fig. 1. Genome
Page 90 and 91: 6 O. N. Reva et al. of which are kn
Page 92 and 93: 8 O. N. Reva et al. compiled into a
Page 94 and 95: 10 O. N. Reva et al. encoded by a c
Page 96 and 97: 12 O. N. Reva et al. systems and ef
Page 98 and 99: 1 2.9 Paper IV: The origins of Vibr
Page 100 and 101: phylogenies based on alternative ho
Page 102 and 103: Figure 1 Phylogenetic tree of the 1
Page 104 and 105: 25000 20000 15000 10000 5000 0 Pan
Page 106 and 107: Gap F 2M 2.5M Gap E 875k 750k 625k
Page 108 and 109: Table 2 A selection of genes locate
Page 110 and 111: Open Access This article is distrib
Page 112 and 113: 1 Comparative Genomics 2.10 Paper V
Page 114 and 115: 4314 74 Tools Abstract: Of the plet
Page 116 and 117: 4316 74 Tools Size distribution of
Page 118 and 119: 4318 74 Tools Genome atlas Intrinsi
Page 120 and 121: 4320 74 Tools Genome atlas Intrinsi
Page 122 and 123: 4322 74 Tools for Comparison of Bac
Page 124 and 125: 4324 74 Tools for Comparison of Bac
Page 126 and 127: 4326 74 Tools information, as genet
Page 128 and 129: Chapter 3 rRNA operons and promoter
Page 130 and 131: tuB murI Fis III Fis II Fis I UP -3
Page 132 and 133: Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
Page 134 and 135: RNA operons and promoter analysis O
Page 136 and 137: Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
Page 138 and 139:
Code Meaning Example C Coding CCCCC
Page 140 and 141:
RNA operons and promoter analysis 3
Page 142 and 143:
P2 -10 -35 UP P1 -10 -35 UP FIS FIS
Page 144 and 145:
1 rRNA operons and promoter analysi
Page 146 and 147:
Using HMMs also simplifies the use
Page 148 and 149:
Information content Information con
Page 150 and 151:
of the annotation. Some of the majo
Page 152 and 153:
where match states stop around 10 c
Page 154 and 155:
1 rRNA operons and promoter analysi
Page 156 and 157:
synthesis in flow cells to simultan
Page 158 and 159:
Read absence. A boolean where ‘on
Page 160 and 161:
Hallin, et al. Figure 4 | The dataf
Page 162 and 163:
Genome homology: Comparing multiple
Page 164 and 165:
ing platform-‐independent Java
Page 166 and 167:
34. Wang H, Noordewier M, Benham CJ
Page 168 and 169:
Chapter 4 Web Services and Interope
Page 170 and 171:
Web Services and Interoperability i
Page 172 and 173:
Page 174 and 175:
Page 176 and 177:
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
Page 184 and 185:
Danmarks Tekniske Universitet AFI,
Page 186 and 187:
Danmarks Tekniske Universitet AFI,
Page 188 and 189:
Appendix C Appendix: Courses C.1 Gl
Page 190 and 191:
D.2 Sample output from queryGenomes
Page 192 and 193:
Appendix: Software 13 w a r n " $ o
Page 194 and 195:
Appendix: Software 109 m y ( $ m i
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
show all

Computational tools and Interoperability in Comparative ... - CBS

Create successful ePaper yourself

Delete template?

Save as template?