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4316 74 Tools Size distribution of prokaryotic genomes (N = 779) AT content distribution of prokaryotic genomes (N = 779) for Comparison of Bacterial Genomes Crenarchaeota (n = 16) Euryarchaeota (n = 35) Nanoarchaeota (n = 1) Acidobacteria (n = 2) Actinobacteria (n = 55) Aquificae (n = 3) Bacteroidetes/chlorobi ( n = 26) Chlamydiae/verrucomicrobia (n = 13) Chloroflexi (n = 7) Cyanobacteria (n = 33) Deinococcus/thermus (n = 4) Firmicutes (n = 155) Fusobacteria (n = 1) Planctomycetes (n = 1) Alphaproteobacteria (n = 94) Betaproteobacteria (n = 61) Gammaproteobacteria (n = 191) Deltaproteobacteria (n = 21) Epsilonproteobacteria (n = 22) Spirochaetes (n = 16) Thermotogea (n = 8) Other archaea (n = 1) Other bacteria (n = 13) 80 70 50 60 AT content (percent) 40 30 12 10 6 8 Genome size (Mbp) 4 2 0 . Figure 1 (a) Box and Whisker plot of genome length distribution for 779 bacterial chromosomes, grouped by phyla. The phylum and the number of chromosomes included are indicated at the left. Each phylum is colored according to our GenomeAtlas website. (b) The distribution of average chromosomal AT content for the same set of bacterial genomes.
eplication tends to be more GC rich, and the region around the replication terminus usually is more ATrich. AT-rich sequences melt more easily than GC-rich sequences, due in part to the extra hydrogen bond present in a GC base pair. Contra-intuitively, this would make the origin of replication the least likely to start replication. However, within the ‘‘large region’’ around the origin of approximately 5% of the chromosome, there is a short stretch of more AT rich basepairs, where the replication origin bubble opens up. Second, and zooming in at genes, the average GC content of intergenic regions is generally lower than that of coding sequences. These regions will melt more readily, are more curved and more rigid than the chromosomal average, in order to enable gene expression (Pedersen et al., 2000, Ussery and Hallin, 2004). This is true for nearly all of the bacterial genomes sequenced, regardless of GC content. In order to calculate relative or local %GC, a window has to be defined (say, investigating 100 basepairs) for which the %GC is calculated. This window is then moved along the genome by singlenucleotide steps, and the %GC is scored related to the middle of each window. These scores can then be graphically represented. A web-based tool for this is available at the Genome Atlas Website 2 in which local %GC can be visualized by color codes as discussed below. 3 Visualization of Genomic Data: The Genome Atlas Genome atlases are circular plots of chromosomes or plasmids (a linear version is available when applicable) on which general properties of the DNA molecule are plotted as colors. Genome atlases are available from our web server 2 for many of the currently sequenced bacterial genomes. > Figure 2 shows a Genome Atlas for the chromosome of Geobacillus kaustophilus strain HTA426 (a thermophilic Firmicute that also contains a plasmid of 4.8 kb). This isolate was obtained from a deep sea sediment of the Mariana Trench in the Pacific Ocean (Takami et al., 2004a, b). Its genome is 3.5 Mbp long and contains 52.1% GC. G. kaustophilus has been suggested to provide a possible solution for paraffin deposition problems with oil production (Sood and Lal, 2008). A Genome Atlas maps four different aspects of the chromosomal DNA sequence in various lanes in a standard manner: DNA structural features are represented in the three outer lanes, all coding sequences are indicated in the next lane, two kinds of repeats are mapped in the next two lanes, and base composition properties are plotted in the two innermost lanes (Jensen et al., 1999). The scale in the center corresponds with the sequence numbering in GenBank. The DNA structural features of the three outermost circles are based on the physical chemical properties of the DNA helix. The annotated genes are given in blue for protein-coding genes oriented clockwise, and red for genes on the other strand (counterclockwise). The tRNA and rRNA genes have their own color. The clockwise strand corresponds with the sequence stored in GenBank (genes on the other strand are annotated as ‘‘complement’’ in there). To identify global repeats (sequences that are repeated somewhere else on the chromosome) we search for the best match of a 100 bp window against the entire chromosome. Searching on the positive strand results in direct repeats (both sequences run in the same direction) whilst searching on the negative strand gives inverted repeats (the two repeat units run in opposite directions). For most of these general properties summarized in a Genome Atlas (structural properties, repeats, base composition) dedicated atlases are also available, where more features are given (such as local and simple repeats in a Repeat Atlas, or 2 http://www.cbs.dtu.dk/services/GenomeAtlas/ Tools for Comparison of Bacterial Genomes 74 4317
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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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Paper VI [Lagesen K, Hallin P] 1 ,
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3.3.3 Refining E. coli and Shigella
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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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1 Comparative Genomics 2.7 Paper II
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166 literally millions of bacterial
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Page 164 and 165: 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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