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Table 3 A dummy PWWM for selected 3-mer pairs at certain distance d. |w 1|, |w 2|, and |w 3| are magnitudes of the weights for the example 3-mer pairs

From: Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization

 

3-mer pairs

 

|w 1|

AAA

GAA

|w 2|

GAA

AGA

|w 3|

AAG

AAA

‘A’

\(\frac {1}{D}(|w_{1}|+|w_{3}|)\)

\(\frac {1}{D}(|w_{1}|+|w_{2}|+|w_{3}|)\)

\(\frac {1}{D}(|w_{1}| +|w_{2}|)\)

\(\frac {1}{D}(|w_{2}|+|w_{3}|)\)

\(\frac {1}{D}(|w_{1}|+|w_{3}|)\)

\(\frac {1}{D}(|w_{1}|+|w_{2}|+|w_{3}|)\)

‘C’

0

0

0

0

0

0

‘G’

\(\frac {1}{D}(|w_{2}|)\)

0

\(\frac {1}{D}(|w_{3})\)

\(\frac {1}{D}(|w_{1}|)\)

\(\frac {1}{D}(|w_{2})\)

0

‘T’

0

0

0

0

0

0

p

1

2

3

4

5

6

  1. ‘A’, ‘C’, ‘G’ and ‘T’ are the rows corresponding to the nucleotides. Position, p∈{1,…,6}. Each cell is divided by D=(|w 1|+|w 2|+|w 3|)