Computational tools and Interoperability in Comparative ... - CBS

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2.17 Pan- and core-genome plot of 10 Campylobacter genomes. For the data
currently available, there seem to exist an equilibrium at close to 600 protein
families. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.18 CorePlot output for 32 Vibrio genomes. . . . . . . . . . . . . . . . . . . . . 24
3.1 The transcription of bacterial genes. . . . . . . . . . . . . . . . . . . . . . . 106
3.2 The promotor structure of the rrnB operon in E. coli. . . . . . . . . . . . . 107
3.3 The –10 and –35 hexamers of the E. coli σ 70 promotor correspond to the
motifs being located on opposite side of the DNA helix. Delition or insertions
of the spacing cases a shift of approx. 36deg per nucleotide. . . . . . 107
3.4 Logo plots showing the initial weight matrices used for searching E. coli
and Shigella genomes: –10 hexamer (a), –35 hexamer (b), UP element (c),
and FIS binding motif (d). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
3.5 Neighbor-joining tree of first 1k bases of all 16S rRNA genes of Yersinia,
Salmonella, Shigella, and E. coli . . . . . . . . . . . . . . . . . . . . . . . . 110
3.6 Profiles showing the maximum Ri(tot) scores of the initial weight matrices
applied to E. coli and Shigella: Unadjusted P1 scores (a), Adjusted P1
scores (b), Unadjusted P2 scores (c), and Adjusted P2 scores (d) . . . . . . 112
3.7 Logos showing the base compostion of P1 and P2 of E. coli genomes, as
identified by initial P1 and P2 scan: P1 –10 hexamer (a), P1 –35 hexamer
(b), P1 UP element (c), P1 FIS binding motif (d), P2 –10 hexamer (e), P2
–35 hexamer (f), P2 UP element (g) . . . . . . . . . . . . . . . . . . . . . . 113
3.8 Average profiles of SIDD energy calculated at five different helix densities
-0.025, -0.035, -0.045, and -0.055. All genes have been aligned at the translation
start. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
3.9 E. coli and Shigella rrnB energy landscape visualized using the heatmap
function. Each vertical column corresponds to a promotor sequence, whereas
the horizontal rows represent average values over 10 bp within each sequence.
Coordinates labeled on the horizontal rows are relative to the 16S
rRNA gene start. The upper heatmaps show P1 whereas the lower heatmaps
show P2. Leftmost heatmaps show P1/P2 model scores in green, whereas
rightmost heatmaps show the SIDD energy in blue. . . . . . . . . . . . . . 116
3.10 Principle workflow of gwBrowser data exchange. . . . . . . . . . . . . . . . 118
3.11 Mapping qualities of sequencing reads to a reference genome while accounting
for the uniqueness of the read. . . . . . . . . . . . . . . . . . . . . . . . 118
3.12 A zoom of the P1 P2 tandem promotor system upstream of the rrnB operon
of E. coli K12. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.1 Screen shot of NCBI Entrez Genome projects web page . . . . . . . . . . . 146
4.2 Schematic layout of a simple SOAP resource, where WSDL and schemas
reside on the same server. WSDL and schemas are read and intepreted
by the SOAP client in order compose the outgoing request and parse the
incoming server response. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
4.3 Schematic layout of the ENCODE pipeline, EPipe. The main program
ensures that as much as possible is dispatched in parrallel. Modules may
either be alignment dependent or not. If the alignment is required to predict
the protein features, the module is not launched until the alignment
algorithm has finished. Modules may either return global features of the
entire protein (e.g. cellular localization), or return positional features (e.g.
phosphorylation sites). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152