Computational tools and Interoperability in Comparative ... - CBS

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Listing 2.8: R code to generate a 2D clustering graphic Comparative Genomics 1 library ( gplots ) 2 postscript ( file =’output .ps ’) 3 data
Genome Comparisons 12 TRNA_SCAN_COUNT LENGTH NGENES RNAMMER_SSU_COUNT ATCONTENT LOC_DIR_REPEAT LOC_INV_REPEAT SR_PERCENT CODING_FRACTION BPPRGENE Escherichia coli SMS−3−5 Escherichia coli O127:H6 str. E2348/69 Escherichia coli E24377A Escherichia coli S88 Escherichia coli SE11 Escherichia coli UMN026 Escherichia coli IAI39 Escherichia coli 55989 Escherichia coli ED1a Escherichia coli UTI89 Escherichia coli CFT073 Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 Salmonella enterica subsp. enterica serovar Newport str. SL254 Salmonella enterica subsp. enterica serovar Agona str. SL483 Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC−B67 Escherichia coli 536 Salmonella enterica subsp. enterica serovar Typhi str. CT18 Serratia proteamaculans 568 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Klebsiella pneumoniae NTUH−K2044 Klebsiella pneumoniae 342 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 Citrobacter koseri ATCC BAA−895 Escherichia coli O157:H7 str. Sakai Escherichia coli O157:H7 EDL933 Escherichia coli O157:H7 str. EC4115 Escherichia coli str. K−12 substr. MG1655 Escherichia coli str. K−12 substr. W3110 Escherichia coli HS Escherichia coli IAI1 Escherichia fergusonii ATCC 35469 Salmonella enterica subsp. arizonae serovar 62:z4,z23:−− Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601 Enterobacter sp. 638 Escherichia coli BL21 Escherichia coli ATCC 8739 Escherichia coli str. K−12 substr. DH10B Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Escherichia coli BW2952 Escherichia coli BL21(DE3) Yersinia pseudotuberculosis YPIII Yersinia pseudotuberculosis PB1/+ Yersinia pseudotuberculosis IP 31758 Yersinia enterocolitica subsp. enterocolitica 8081 Yersinia pseudotuberculosis IP 32953 Shigella boydii Sb227 Shigella dysenteriae Sd197 Escherichia coli APEC O1 Shigella flexneri 2a str. 301 Shigella sonnei Ss046 Shigella flexneri 5 str. 8401 Shigella flexneri 2a str. 2457T Shigella boydii CDC 3083−94 Edwardsiella ictaluri 93−146 Cronobacter sakazakii ATCC BAA−894 Erwinia tasmaniensis Et1/99 Photorhabdus luminescens subsp. laumondii TTO1 Photorhabdus asymbiotica Proteus mirabilis HI4320 Pectobacterium atrosepticum SCRI1043 Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 Pectobacterium carotovorum subsp. carotovorum PC1 Dickeya zeae Ech1591 Dickeya dadantii Ech703 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Yersinia pestis Angola Yersinia pestis CO92 Yersinia pestis Antiqua Yersinia pestis KIM Yersinia pestis Nepal516 Yersinia pestis biovar Microtus str. 91001 Yersinia pestis Pestoides F Sodalis glossinidius str. morsitans Buchnera aphidicola str. Cc (Cinara cedri) Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis Candidatus Blochmannia floridanus Candidatus Blochmannia pennsylvanicus str. BPEN Buchnera aphidicola str. Sg (Schizaphis graminum) Buchnera aphidicola str. Bp (Baizongia pistaciae) Buchnera aphidicola str. APS (Acyrthosiphon pisum) Buchnera aphidicola str. Tuc7 (Acyrthosiphon pisum) Buchnera aphidicola str. 5A (Acyrthosiphon pisum) −1 −0.5 0 0.5 1 Value Figure 2.5: 2D-clustering showing 87 Enterobacteriaceae. Color Key
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 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
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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
Page 82 and 83: 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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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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tuB murI Fis III Fis II Fis I UP -3
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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
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RNA operons and promoter analysis O
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Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
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Code Meaning Example C Coding CCCCC
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RNA operons and promoter analysis 3
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P2 -10 -35 UP P1 -10 -35 UP FIS FIS
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1 rRNA operons and promoter analysi
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Using HMMs also simplifies the use
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Information content Information con
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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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