Doubt on genomic code for nucleosome positioning? I was reading "A genomic code for nucleosome positioning" (by Eran Segal et al). And I am having 2 doubts. !enter image description here The figure(b) in this image from the paper shows the graph of fraction (3-bp moving average) of AA/TA/TT dinucleotides of nucleosome dna sequence they analysed statistically as far as I understand. What is 3-bp moving average here? I also don't understand how they chose 0th position (the so called dyad). Also what does it mean to have oscillations (correlation?) in this graph? * * * UPDATE : I am adding some supplementary information related to finding the dinucleotide fractions. Still I don't understand why is the fraction found so? !enter image description here

Dyad is the centre of the DNA that is wrapped around the nucleosome core (It basically is the centre of symmetry of the nucleosome). It is a common practice to set it at 0 thereby making incoming DNA half, negative and outgoing DNA half, positive.

By oscillations the authors mean that there is a periodic repeat of A/T dinucleotide. IMO it is actually not correct to call it oscillation which is mostly used in a time course dynamical sense.

I guess this is what is meant by the **3-nt moving average** :

You have conditional dinucleotide probabilities for each position (As shown in the figure). Now you calculate the A/T dinucleotide probability which is:


P[A/T] = PAA + PAT + PTT + PTA

Now you find the moving average for 3 steps:


MA(n) = (1/3)×(PA/T + PA/T + PA/T)

_where **n** is the nth position of the DNA_