PING

"PING" (Precise INucleosome positioninG) is a model-based software tool designed to predict nucleosome positions using MNase-Seq and MNase—or sonicated-ChIP-Seq data. By leveraging advanced modeling techniques, PING significantly improves on existing methods such as NPS and TemplateFilter, particularly in terms of scalability, accuracy, and its ability to deliver robust predictions even in cases of low read density.

A key feature of PING is its capacity to extract meaningful biological insights from widely available sonicated data, achieving a spatial resolution sufficient for biological interpretation.

Topic

ChIP-seq;Sequencing;Immunoprecipitation experiment;DNA binding sites

Detail

  • Operation: Statistical inference

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 2.46.0

  • Credit: The National Institutes of Health, the Natural Sciences and Engineering Research Council of Canada.

  • Input: -

  • Output: -

  • Contact: Renan Sauteraud renan.sauteraud@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.
  • Zhang X, et al. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. 2012; 7:e32095. doi: 10.1371/journal.pone.0032095
  • https://doi.org/10.1371/journal.pone.0032095
  • PMID: 22393380
  • PMC: PMC3290535

Download and documentation

< Back to DB search