Nucleosome positioning: resources and tools online

TL;DR

This review provides a comprehensive guide to online resources, datasets, and computational tools for nucleosome positioning analysis, facilitating research in genome organization and gene regulation.

Contribution

It compiles and curates a detailed, accessible list of nearly 300 datasets and over 40 computational tools for nucleosome positioning analysis.

Findings

Curated list of 300 experimental datasets available online.

Over 40 computational tools for nucleosome analysis.

Resource maintained at http://generegulation.info.

Abstract

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.