Prediction of nucleosome position
Prediction of nucleosome position by using DNA dinucleotide nucleosome pattern
Nucleosome position can be predicted by alignment of nucleosome dinucleotide pattern 147 bp long with DNA sequence. Correlation between 16 dinucleotides matrix (nucleosome pattern) and DNA sequence is a measure of affinity DNA to histone octamer. Center of aligned DNA to the matrix corresponds to position of nucleosome. Position of the maximal positive correlation between matrix and DNA sequence corresponds to the best position of nucleosome. More than one position of nucleosome can be predicted if DNA sequence is long enough. Average distance between nucleosomes in human genome is 180-200 bp. The minimal distance between nucleosomes (their centers) should be 147 bp, length of nucleosome sequence, + 10-20bp linker between nearest nucleosomes.
We designed special script to predict position (or positions if sequence is long enough) of nucleosome on DNA sequence.