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nuScore: a web-interface for nucleosome positioning predictions.

Michael Y Tolstorukov1, Vidhu Choudhary, Wilma K Olson

  • 1Harvard-Partners Center for Genetics and Genomics, Brigham and Women's Hospital, Boston, MA 02115, USA. tolstorukov@gmail.com

Bioinformatics (Oxford, England)
|May 1, 2008
PubMed
Summary
This summary is machine-generated.

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We developed nuScore, a web tool predicting how DNA sequences influence nucleosome positioning by calculating histone-DNA binding energy. This helps understand DNA organization within cells.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biophysics

Background:

  • Nucleosome positioning is crucial for DNA accessibility and gene regulation.
  • Predicting nucleosome arrangement on DNA sequences is a significant biological challenge.

Purpose of the Study:

  • To present a novel web-interface, nuScore, for estimating histone-DNA binding affinity.
  • To predict nucleosome arrangement on a given DNA sequence using biophysical principles.

Main Methods:

  • The approach assesses the energy cost of DNA deformation required for wrapping around the histone core.
  • Utilizes threading calculations with selectable structural templates and options for random sequence analysis.

Main Results:

  • A functional web interface (nuScore) is available for predicting nucleosome positioning.

Related Experiment Videos

  • The tool quantifies the energetic favorability of DNA sequences for nucleosome formation.

    • Conclusions:

    • nuScore provides a valuable tool for researchers investigating sequence-directed nucleosome mapping.
    • The methodology offers insights into the biophysical determinants of DNA organization within the nucleus.