Table 1

Comparison of original and new mono-nucleotide PWM
A)
1 2 3 4 5 6
A 25 0 61 0 39 15
T 20 0 1 58 19 8
G 4 62 1 5 4 37
C 14 1 0 0 1 3
A 0.40 0.0 0.97 0.0 0.62 0.24
T 0.32 0.0 0.02 0.92 0.30 0.17
G 0.06 0.98 0.02 0.08 0.06 0.59
C 0.22 0.02 0 0.0 0.02 0.05
A 0.00 -3.83 0.00 -4.12 0.00 -0.55
T -0.021 -3.82 -4.10 0.00 -0.79 -1.16
G -2.19 0.00 -4.47 -2.81 -2.63 0.00
C -0.92 -4.11 -4.51 -4.47 -4.10 -2.50
a/t G A T A g/a
B)
1 2 3 4 5 6
A 27 0 66 0 43 16
T 22 0 1 63 20 8
G 4 67 1 5 4 41
C 15 1 0 0 1 3
A 0.40 0.0 0.97 0.0 0.63 0.24
T 0.32 0.0 0.01 0.93 0.29 0.12
G 0.06 0.99 0.01 0.07 0.07 0.62
C 0.22 0.01 0.0 0.0 0.01 0.04
A 0.00 -3.83 0.00 -4.13 0.00 -0.59
T -0.19 -3.82 -3.48 0.00 -0.76 -1.27
G -2.26 0.00 -3.84 -2.9 -2.73 0.00
C -0.93 -3.49 -4.52 -4.48 -3.4 -2.61
a/t G A T A g/a

A. Original mono-nucleotide nucleotide counts (top panel), frequency table (middle panel) and calculated PWM (bottom panel). The frequency table and the PWM is calculated from 63 motifs adopted from Jaspar. The first row represents the column index of the matrices. The last row represents the consensus of the original PWM.

B. Optimized mono-nucleotide frequency table and PWM. The nucleotide counts (top panel) and frequency table (middle panel) calculated from the 68 sites obtained by the optimization process in the functional window -7 to 0 was used to build the optimized PWM. The bottom panel is the calculated PWM. The first row represents the column index of the matrices. The last row represents the consensus of the optimized PWM.

Nandi and Ioshikhes

Nandi and Ioshikhes BMC Genomics 2012 13:416   doi:10.1186/1471-2164-13-416

Open Data