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Hallin, et al. Figure 4 | The dataflow of the GeneWiz browser service. 1) The selected reference genome and the lanes to be included are defined via the web interface. 2) The request is sent to the analysis server that handles the calculations. 3) When the job is finished, the web page redirects to the applet viewer that allows the user to navigate and edit the plot layout. Premade atlases The genome sequences stored in the CBS Genome Atlas Database [25] are synchronized with NCBI Entrez genome projects and have been pre-‐ processed for all of the eight standard atlases mentioned above. This allows the user to select from currently 1,636 pre-‐binned replicons from 864 prokaryotic sequencing projects, searchable by replicon name, GenBank accession number, or organism name (http://www.cbs.dtu.dk/-‐ servic-‐ es/gwBrowser/precalc/) Results Evaluation of re-sequencing quality Three re-‐sequenced bacterial genomes were ex-‐ amined, one genome sequence was generated us-‐ ing the Illumina GA technology, whereas two ge-‐ nome sequences were generated utilizing the 454-‐ Titanium technology (Table 3). The public se-‐ quence was selected as reference for mapping the re-‐sequencing reads using the GeneWiz browser tool. The randomness in fragmentation was esti-‐ mated by comparing the experimental data with in-silico digestions, generated at 40X coverage using read lengths between 30 to 5,000 bp. A good correspondence between the in-silico and experi-‐ mental reads suggests little bias towards certain chromosomal regions (Figure 5, panel A). The as-‐ sembled contigs provided by 454 (C. jejuni and E. coli) are mapped to the reference genome using BLAST and annotated in the perimeter of the at-‐ lases (two leftmost atlases in Figure 5, panel A+B). The detailed atlas of the experimental data (true reads), are shown in Figure 5, panel B. Panel C shows quality/count of reads plotted as a function of read position. Note that the read quality de-‐ creases the further the distance from the begin-‐ ning of the read. http://standardsingenomics.org 209
GeneWiz browser Table 3 Sequencing details of three bacterial genomes, two of which were re-sequenced using 454-Titanium and one with Illumina GA technology. E. coli K12 MG1655 C. jejuni NCTC11168 S. typhi Ty2 Strain id ATCC: 700926D-5 ATCC: 700819D-5 ERA000001 Technology 454-Titanium 454-Titanium Illumina GA II Read count 538,784 502,438 1,650,370 Avg read length ((std. dev) 522 (=53) 598 (=75) 51 (=0) Truncated length 600 600 35 Coverage 61X 183X 18X Genome size 4,639,675 bp 1,641,481 bp 4,791,961 bp Accession and original Reference U00096 [26] AL111168 [27] AE014613 [28] Figure 5 | Panel A: The maximum uniqueness quality is shown for the actual reads (green-to-blue lane) plotted in the outermost lanes, using the published genome as a reference. The following lanes show in-silico digestions at 40 X coverage (red-to-blue lane), using read lengths 30, 50, 70, 200, 500, 1,000, 1,000, and 5,000 bases. Panel B shows the weighted coverage, agreement with reference, maximum uniqueness quality, information content, read absence, and AT content. All six plots can be accessed for zooming via the supplemental data section. Panel C displays the read count (green, secondary ordinate) and read quality (red, primary ordinate) as a function of read length. Note that read counts differ within the three datasets, resulting in different scales on the secondary ordinate. For the two 454-Titanium sets (C. jejuni and E. coli K12), an assembly was provided which allows a mapping of contigs to the reference genome. These marks are shown in gray in the perimeter of these plots. Red marks indicate contigs with two or more hits in the reference. 210 Standards in Genomic Sciences
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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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170 resistance genes on mobile gene
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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176 Fig. 5 Genome length distributi
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180 reasons why organisms remain un
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182 A final problem has to do with
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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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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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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
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