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Bioinformatics Advance Access published online on April 29, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn212
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

nuScore: a web-interface for nucleosome positioning predictions

Michael Y. Tolstorukov 1,*, Vidhu Choudhary 2, Wilma K. Olson 3, Victor B. Zhurkin 4 and Peter J. Park 1,2,*

1Harvard-Partners Center for Genetics and Genomics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
2Children Hospital Informatics Program, Boston, Massachusetts 02115, USA
3Wright-Rieman Laboratories, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
4Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892, USA

*To whom correspondence should be addressed. Prof. Peter J. Park, E-mail: peter_park{at}harvard.edu


  Abstract

Summary: Sequence-directed mapping of nucleosome positions is of major biological interest. Here, we present a web-interface for estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. Our approach is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface. The interface allows the user to specify a number of options such as selecting from several structural templates for threading calculations and adding random sequences to the analysis.

Availability: The nuScore interface is freely available for use at http://compbio.med.harvard.edu/nuScore.

Supplementary information: The site contains user manual, description of the methodology, and examples.

Contact: peter_park{at}harvard.edu; tolstorukov{at}gmail.com

Associate Editor: Prof. Martin Bishop

Received on January 2, 2008; revised on April 25, 2008; accepted on April 26, 2008

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