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Fig. 5 BLASTatlas of Clostridium botulinum F strain Langeland: Lanes show genome homology of (starting from the outermost lane): C. acetobutylicum ATCC 824, C. beijerinckii NCIMB 8052, C. botulinum A str. ATCC 19397, C. botulinum A ATCC 3502, C. botulinum A str. Hall, C. difficile 630, C. kluyveri DSM 555, C. novyi NT, C. perfringens ATCC 13124, C. perfringens SM101, C. perfringens str. 13, C. tetani E88, C. thermocellum ATCC 27405, and Clostridium phage c-st genome. Inside of the annotation circle are shown global direct repeats, global inverted repeats, stacking energy, and percent AT. Blue and red annotations are coding sequences on plus and minus strand, whereas green and turquoise are rRNA and tRNA, genes respectively. The two toxin components NTNH and BoNT/A1 that are identified on phage c-st are present in the reference genome at positions 880 kb and 883 kb, respectively (marked ‘cst’). The presence of the two is visible as a thin blue band on the c-st blast lane. The lower part of the figure shows a zoom of the region around 2635 kb, providing an example of a gene cluster which appears to be conserved throughout the C. botulinum strains and partly within the C. difficile 630. phages or plasmids present in the genome. The proteins encoded by the 185 kb neurotoxin-converting bacteriophage c-st are labelled, as well as a region which is zoomed in the second panel in Fig. 5. The accession numbers, total size and total number of genes within each lane can be seen in Table 2. There are several items of interest which can be seen in Fig. 5. First, the rRNA operons can be quite readily seen, near the top part of the chromosome map, labeled turquoise; these rRNA operons are more GC rich (hence less red in the inner-most lane), have direct and inverted repeats (the next two lanes), and are not shown in the proteome comparison lanes (since these genes do not encode proteins). As expected, the circle representing the c-st phage shows little match for most of the C. botulinum genome, at the protein level. In general, the two other C. botulinum genomes (both in blue) have the highest similarity to the reference C. botulinum genome (also shown as a circle). In this case it is used as an internal control: all of the proteins should show a match for this lane, since the reference genome is blasted against itself. Another interesting observation is the upper-lefthand part of the genome which seems to have more homology to other Clostridium genomes, in particular showing many matches to the C. perfringens genomes (green circles), compared to the rest of the genome. Application in metagenomics The genera of Prochlorococcus belongs to the cyanobacteria and is one of the most abundant photosynthetic organisms of the ocean. It plays an important role in the planet’s carbon cycle and has adapted to the various light and oxygen conditions present at the various depths. 11 As of the end of January 2008, eleven Prochlorococcus marinus genomes are publicly available and we have included all encoded proteins of these data with the seven metagenomic read collections from the ALOHA station near Hawaii, 12 as shown in Table 3. The strain of P. marinus strain MIT 9303 has the largest genome of all 368 | Mol. BioSyst., 2008, 4, 363–371 This journal is c The Royal Society of Chemistry 2008
Table 3 A list of all strains/sample names and their accession numbers used in the metagenomic comparison. The list is sorted by sampling depth Source Size Origin Accession/sample Ref. Depth P. marinus str. MIT 9515 1 704 176 (1906 proteins) Tropical Pacific CP000552 Unpublished Surface P. marinus str. MIT 9215 1 738 790 (1983 proteins) Equatorial Pacific CP000825 Unpublished Surface P. marinus str. MED4 1 657 990 (1936 proteins) Mediterranean Sea BX548174 21 4 m JGI_SMPL_HF10_10-07-02 7 482 668 (7842 contigs) North Pacific Subtropical Gyre — 12 10 m P. marinus str. NATL1A 1 864 731 (2193 proteins) North Atlantic CP000553 Unpublished 30 m P. marinus str. NATL2A 1 842 899 (2163 proteins) North Atlantic CP000095 Unpublished 30 m P. marinus str. AS9601 1 669 886 (1921 proteins) Arabian Sea CP000551 Unpublished 50 m JGI_SMPL_HF70_10-07-02 10 828 386 (10 999 contigs) North Pacific Subtropical Gyre — 12 70 m P. marinus str. MIT 9211 1 688 963 (1855 proteins) Equatorial Pacific CP000878 21 83 m P. marinus str. MIT 9301 1 641 879 (1907 proteins) Sargasso Sea CP000576 Unpublished 90 m P. marinus str. MIT 9303 2 682 675 (2997 proteins) Sargasso Sea CP000554 Unpublished 100 m P. marinus str. SS120 1 751 080 (1882 proteins) Sargasso Sea AE017126 22 120 m JGI_SMPL_HF130_10-06-02 6 091 784 (6812 contigs) North Pacific Subtropical Gyre — 12 130 m P. marinus str. MIT 9312 1 709 204 (1962 proteins) Equatorial Pacific CP000111 Unpublished 135 m P. marinus str. MIT MIT9313 2 410 873 (2273 proteins) Gulf Stream BX548175 21 135 m JGI_SMPL_HF200_10-06-02 7 829 659 (8286 contigs) North Pacific Subtropical Gyre — 12 200 m JGI_SMPL_HF500_10-06-02 8 764 642 (9027 contigs) North Pacific Subtropical Gyre — 12 500 m JGI_SMPL_HF770_12-21-03 11 811 597 (11 479 contigs) North Pacific Subtropical Gyre — 12 770 m JGI_SMPL_HF4000_12-21-03 11 028 821 (11 229 contigs) North Pacific Subtropical Gyre — 12 4000 m currently available sequences (2.7 Mb) and was therefore used as reference in this comparison. BLAST hits between the reference and the encoded proteins of all the P. marinus genomes included were generated with the BLASTp algorithm, whereas hits between the reference proteins and the DNA reads of the metagenomic samples were generated using the tBLASTn algorithm. tBLASTn was used to avoid the gene prediction step of the metagenomic samples and to allow a rough estimate of the coding potential of these samples. All lanes are sorted according to the water depth at which the samples were collected (see Fig. 6). The Perl code for constructing this plot using web services is provided on the service homepage. Discussion The BLASTatlas method can assist biologists in finding regions along the chromosome which are conserved (or not). This information is useful for several Fig. 6 BLASTatlas showing fully sequenced Prochlorococcus genomes (green) and the seven ALOHA metagenomic samples (blue). Outermost lanes represent samples closer to the ocean surface. This journal is c The Royal Society of Chemistry 2008 Mol. BioSyst., 2008, 4, 363–371 | 369
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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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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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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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