Abstract
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
5-22-2014
Document Type
Thesis
Student Type
Graduate
Degree Name
Bioinformatics (MS)
Department, Program, or Center
Thomas H. Gosnell School of Life Sciences (COS)
Advisor
Feng Cui
Advisor/Committee Member
Paul Craig
Advisor/Committee Member
Gary R. Skuse
Recommended Citation
Alharbi, Bader, "NuMap: a web platform for prediction of nucleosome rotational and translational positioning at high resolution" (2014). Thesis. Rochester Institute of Technology. Accessed from
https://repository.rit.edu/theses/9117
Campus
RIT – Main Campus
Comments
Physical copy available from RIT's Wallace Library at QP625.N87 A54 2014