Aligning nucleosome occupancy profiles

At this point we have:

• the nucleosome occupancy for each strain,
• the sequence alignment of the strain genomes,

so we can try now to look at the differences in nucleosome occupancy between the two strains. To do that, we will simply align the two nucleosome occupancy profiles based on what we already know about the sequence alignment. By nucleosome occupancy profiles we mean here the most-likely nucleosome occupancy profiles of the two strains (as obtained from the Viterbi algorithm (NMhmmvit) on each chromosome).

Figure: