Computational tools and Interoperability in Comparative ... - CBS

Conservation of regulatory elements
Ri
Ri
−15 −10 −5 0 5 10
−10 −5 0 5 10 15
P1: Raw combined scores, −10,−35, UP (E.coli) (N=63)
−500 −400 −300 −200 −100 0
Position relative to 16S gene start
(a)
P2: Raw combined scores, −10,−35, UP (E. coli) (N=63)
−500 −400 −300 −200 −100 0
Position relative to 16S gene start
(c)
Ri
Ri
−15 −10 −5 0 5 10 15
−10 −5 0 5 10 15
P1: Adjusted combined scores, −10,−35, UP (E.coli) (N=63)
−500 −400 −300 −200 −100 0
Position relative to gene start
(b)
P2: Adjusted combined scores, −10,−35, UP (E. coli) (N=63)
−500 −400 −300 −200 −100 0
Position relative to gene start
Figure 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)
3.3.2 Iterating weight matrix frequencies
The program iscan was developed to query a given DNA sequence and for every position in
this sequence calculate the maximum Ri(tot) that can be obtained by trying out different
spacing configuraitons within a specified window. The iscan algorithm aligns the first
matrix with the query (in this case the –10 hexamer) and tries all distances between 13
and 19 nucleotides towards the –35 hexamer, using 16 nucleotides as the center. Then
the program locks the optimal of those distances, and continues with the next box (in
this case the the UP element) until all elements have been included. For source code, see
appendix D.5. The spacing configuration of the two models is shown in figure ??.
The maximum Ri(tot) values of all operons were stacked and average and standard
deviation values were plotted as function of position. Because the distance between P1/P2
and the 16S gene varies slightly, the unadjusted plots appear noisy. By shifting the plots
slightly by aligning to local maxima around P1 and P2 renders the P1 and P2 model scores
sharper (see figure 3.6).
3.3.3 Refining E. coli and Shigella models
All peaks of Ri(tot) around the regions of P1 and P2 have been collected, and the P1 and
P2 models were refined by adjusting matrix parameters according to the observed base
frequencies in the hits obtained. The logo plots of are shown in figure 3.7
112
(d)