Nucleosome positioning: resources and tools online
It provides a practical resource for researchers in genomics and bioinformatics, but is incremental as it reviews existing tools without introducing new methods.
This review addresses the challenge of navigating the extensive online resources for nucleosome positioning by compiling a guide to nearly 300 experimental datasets and over 40 computational tools, with a manually curated list maintained at a dedicated website.
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.