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Table 3 Information weight matrix used to search for metboxes

From: The MetJ regulon in gammaproteobacteria determined by comparative genomics methods

 

Count1

Riw (bits per base)2

 

1 (8)

2 (7)

3 (6)

4 (5)

1 (8)

2 (7)

3 (6)

4 (5)

A

634

156

721

37

1.61

-0.42

1.79

-2.49

C

6

25

84

573

-5.12

-3.06

-1.31

1.46

G

135

560

27

4

-0.62

1.43

-2.95

-5.70

T

57

91

0 > 13

218

-1.87

-1.19

-7.70

0.07

  1. 1 This refers to the number of times each base occurred at each position in the (symmetrized) metbox. The frequency used in Equation 1 is the count divided by the total number of half-metboxes: 832. The consensus sequence is highlighted in bold.
  2. 2 Riw is the information content for each base at each position calculated using Equation 1. The consensus sequence is highlighted in bold.
  3. 3 The occurrence of T (A) at position 3 (6) was zero, so this was changed to 1 to allow the log to be taken.
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BMC Genomics

ISSN: 1471-2164

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