Bader Alharbi


Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimental mapping of nucleosomal arrangements signifies the need for computational approaches to predict nucleosome positioning at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, W/S and YR schemes, for the rotational and translational positioning of nucleosomes respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation providemultiple layout options to adjust the scoring graphs and then exports the results into multiple formats including PDF, Excel, and CSV.

Library of Congress Subject Headings

Eukaryotic cells--Genetics; Genetic transcription--Data processing; Genetic regulation--Data processing

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Feng Cui

Advisor/Committee Member

Paul Craig

Advisor/Committee Member

Gary R. Skuse


Physical copy available from RIT's Wallace Library at QP625.N87 A54 2014


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