Computational tools and Interoperability in Comparative ... - CBS

Code Meaning Example
C Coding CCCCCCCCCCCCC
> Annotation start on forward strand .....>CCCC...
< Annotation start on reverse strand ...CCCCTTT.....
t 5S rRNA ..tttssss......
l 23S rRNA ...lllllcodesearch −cod U00096 . cod . gz −seq U00096 . fsa −pat ’(.{5 ,5} > s {1 ,1}) ’
2 223773..223779 AAATTGA
3 3939833..3939839 AAATTGA
4 4033556..4033562 AAATTGA
5 4164684..4164690 AAATTGA
6 4206172..4206178 AAATTGA
7 3426782..3426776 ATTGAAG
8 2729177..2729171 ATTGAAG
9 >codesearch −cod U00096 . cod . gz −dat U00096 . sidd35 . gz : 1 , 4 −pat
’(.{5 ,5} > s {1 ,1}) ’\
10 −format ’%0.2f ’ | tab2tbl −−window = ’ −5 ,2 ’ −org ’ E . coli K12 ’ −col
blue
11 def org col −5 −4 −3 −2 −1 1 2
12 223773..223779 E . coli K12 blue 7.93 7.93 7.94 8.00 8.26 8.28 8.37
13 3939833..3939839 E . coli K12 blue 7.91 7.90 7.92 7.99 8.25 8.28 8.36
14 4033556..4033562 E . coli K12 blue 7.83 7.83 7.85 7.92 8.19 8.22 8.32
15 4164684..4164690 E . coli K12 blue 7.85 7.85 7.87 7.95 8.21 8.25 8.34
16 4206172..4206178 E . coli K12 blue 7.91 7.91 7.92 7.99 8.26 8.28 8.37
17 3426782..3426776 E . coli K12 blue 7.91 7.93 7.99 8.26 8.28 8.37 8.73
18 2729177..2729171 E . coli K12 blue 7.91 7.93 7.99 8.26 8.28 8.37 8.72
Using heatmap to generate energy landscape
The R function heatmap described in chapter 2, was used to compare both SIDD profiles
and the profiles of P1/P2 model scores. All promotor sequences were aligned first according
to the peak score of the P1 model (near the expected site of P1) and second according to
the peak score of the P2 model (near the expected site of P2). In figure 3.9 the model scores
are visualized using the heatmap function on the green, heatmaps on the left, whereas the
rightmost heatmaps contain the SIDD energies (blue) of the aligned promotor sequences.
This analysis show that a deep drop in the SIDD energy occurs for approximately half of
the promotor sequences, near the P1 site.
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