Software (see also our lab github)

IC-Finder : Segmentations of HiC maps into hierarchical interaction compartments.

The spatial organization of the genome plays a crucial role in the regulation of gene expression. Recent experimental techniques like HiC have emphasized the segmentation of genomes into interaction compartments that constitute conserved functional domains participating in the maintenance of a proper cell identity. Here, we propose a novel method, IC-Finder, to identify interaction compartments (IC) from experimental Hi-C maps. IC-Finder is based on a hierarchical clustering approach that we adapted to account for the polymeric nature of chromatin.  IC-Finder proposes two original options: a probabilistic description of the inferred compartments and the possibility to explore the various hierarchies of chromatin organization. IC-Finder provides a robust and generic tool to uncover the general principles of 3D chromatin folding and their influence on gene regulation.

A MATLAB/GNU OCTAVE subroutine is available here. Data for a benchmark of in silico HiC maps can be found here. Data used to learn the IC-Finder default parameters are available here.

How to cite: N. Haddad, C. Vaillant & D. Jost (2017) IC-Finder: inferring robustly the hierarchical organization of chromatin folding. Nucleic Acids Research, 45: e81.

Twist-DNA : Computations of base-pair and bubble opening probabilities for any DNA sequence at given temperature, superhelical stress and salt concentration.

Local opening of the DNA double-helix is required in many fundamental biological processes and is in part controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed Twist-DNA, a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties to other available datasets.

Codes are available here. Data for the genomes of E. coli and B. subtilis in physiological conditions (Temperature 37C, Salt concentration 0.1 M and Superhelical density -0.06) are available here in BED format.

A Twist-DNA wrapper for Galaxy has been developed by Björn Grüning. It is integrated in the Galaxy Toolshed and is also available here.

How to cite: D. Jost (2013) Twist-DNA: computing base-pair and bubbles opening probabilities in genomic superhelical DNA. Bioinformatics, 29: 2479-2481.