Articolo in rivista, 2019, ENG, 10.1109/TCBB.2018.2838669

ChromStruct 4: a Python code to estimate the chromatin structure from Hi-C data

Caudai C.; Salerno E.; Zoppè M.; Merelli I.; Tonazzini A.

CNR-ISTI, Pisa, Italy; CNR-ISTI, Pisa, Italy; CNR-IFC, Pisa, Italy; CNR-ITB, Milan, Italy; CNR-ISTI, Pisa, Italy

A method and a stand-alone Python(TM) code to estimate the 3D chromatin structure from chromosome conformation capture data are presented. The method is based on a multiresolution, modified-bead-chain chromatin model, evolved through quaternion operators in a Monte Carlo sampling. The solution space to be sampled is generated by a score function with a data-fit part and a constraint part where the available prior knowledge is implicitly coded. The final solution is a set of 3D configurations that are compatible with both the data and the prior knowledge. The iterative code, provided here as additional material, is equipped with a graphical user interface and stores its results in standard-format files for 3D visualization. We describe the mathematical-computational aspects of the method and explain the details of the code. Some experimental results are reported, with a demonstration of their fit to the data.

IEEE/ACM transactions on computational biology and bioinformatics (Online) 16 (6), pp. 1867–1878

Keywords

Chromosome conformation capture, Chromatin configuration, Bayesian estimation

CNR authors

Caudai Claudia, Zoppe Monica Maria, Merelli Ivan, Salerno Emanuele, Tonazzini Anna

CNR institutes

IFC – Istituto di fisiologia clinica, ISTI – Istituto di scienza e tecnologie dell'informazione "Alessandro Faedo", ITB – Istituto di tecnologie biomediche

ID: 387460

Year: 2019

Type: Articolo in rivista

Creation: 2018-05-23 14:16:14.000

Last update: 2021-04-08 00:28:36.000

External IDs

CNR OAI-PMH: oai:it.cnr:prodotti:387460

DOI: 10.1109/TCBB.2018.2838669

Scopus: 2-s2.0-85047190075

ISI Web of Science (WOS): 000507924300009