Reconstruction of 3D chromatin structure from chromosome conformation capture data (Release 3.1)

Salerno E., Caudai C.

Chromosome conformation capture  Computational biology  Python source code 

This Python code has a command-line and a GUI versions, and provides an estimate of the 3D structure of the chromatin fibre in cell nuclei from the contact frequency data produced by a 'Chromosome conformation capture' experiment. The only input required is a text file containing a general real matrix of contact frequencies. In the command-line version, the related genomic resolution, along with a few geometric parameters and the parameters for tuning the estimation algorithm must be set in advance in a special section of the source code. In the GUI version, all the tuneable parameters are made available in the user interface. The whole fibre is divided in independent segments, whose structures are estimated and modelled as single elements of a lower-resolution fibre that is treated recursively in the same way, until it cannot be divided anymore into independent segments. The full-resolution chain is then reconstructed by another recursive procedure. See the Readme file and the cited references for more detail.

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