What it is
Nucleosome eXclusion Sensor (NXSensor) is a tool for finding regions of DNA sequences that are likely to be nucleosome-free. Nucleosomes are made up of 8 histones that form together into a sort of bead-like structure. It has been shown that it takes 147 nucleotides to wrap around a nucleosome. The basic idea behind NXSensor is that the DNA sequence which wraps around the nuclosome needs to have a certain degree of flexibility. DNA flexibility is a necessary (though not the only, and also not sufficient) condition for nucleosome formation. It is known that the intrinsic curvature of a piece of DNA depends on its sequence, and we use that knowledge to find DNA sequences that are fairly rigid. Regions of DNA that have several rigid sequences close to each other are likely to be nucleosome-free. We call these rigid sequences "nucleosome-exclusion sequences."
NXSensor software is currently not optimized for speed. We apologize if it appears somewhat slow.