Nucleome Browser use nucle3D format to represent DNA 3D Structure.
An example of a nucle3D file is shown below. Each file represents a 3D structure of chromatin with a fixed bin size. The first several rows (tab-delimited) indicate the name (TITLE) of this structure, genome assembly version (GENOME), and bin size (BINSIZE). Note that the nucle3D format requires that all chromatin segments have the same bin size and those chromatin segments are non-overlapping. For each chromosome, a row starting with CHR tells to which chromosome the following bins belongs. Then, the following bins show the bin-id (0-base) and XYZ positions of this chromatin segment. For example, if the bin-size is 100kb, the first bin (0 to 100kb) should have bin-id 0. Bin-id and XYZ positions are separated by comma as shown in the example below. You can skip bins if there is no data on those bins.
Support for variable bin sizes, diploid genome, and visualization of nuclear bodies will be added in the next version of the Nucle3D format.
TITLE [NAME] # Tab split
GENOME hg38 # Tab split
BINSIZE [binsize]
CHR chr1 # Tab split
i,x,y,z
i,x,y,z
..
CHR chr2
..
You can use nucleserver to host custom 3D structural data. Please follow the instruction on nucleserver repo to install it.
You can put all 3D structural data in a folder (e.g. 3D). You can then start a data service to host these data using the following command.
# assume the folder 3D contains the structural data, each file represent a 3D structure
nucleserver file --root 3D
You should see a message like this "Please open http://127.0.0.1:8611". This means that all the 3D structural data can be retrieved under URL http://127.0.0.1:8611/get/. You can copy the URL of the 3D structural data into the input data box in the 3D structure panel of the Nucleome Browser.
We have also included a demo data in this repo. You can start from this demo. Once you clone this repo and install nucleserver. You can start a 3D data server using the following command .
nucleserver file --root data
You can then copy the following URL of the 3D structure data (http://127.0.0.1:8611/get/K562.nucle3d) into the input data box in the 3D structure panel. You will then see the 3D structure.
