nuScore: a web-interface for nucleosome positioning predictions

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 imposi...

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Bibliographic Details
Published in:Bioinformatics 2008-06, Vol.24 (12), p.1456-1458
Main Authors: Tolstorukov, Michael Y., Choudhary, Vidhu, Olson, Wilma K., Zhurkin, Victor B., Park, Peter J.
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Biological and medical sciences
Chromosome Mapping - methods
Computer Simulation
Fundamental and applied biological sciences. Psychology
General aspects
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Genetic
Molecular Sequence Data
Nucleosomes - genetics
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
User-Computer Interface
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Description
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. Contact: peter_park@harvard.edu; tolstorukov@gmail.com Supplementary information: The site contains user manual, description of the methodology and examples.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn212