Predicting nucleosome positioning using a duration Hidden Markov Model

Background: The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software tool for predicting nucleosome positioning can help understanding how a genome's nucleosome organization may facilitate genome function. Results: We present a duration Hidden Markov model for nucleosome positioning prediction by explicitly modeling the linker DNA length. The nucleosome and linker models trained from yeast data are re-scaled when making predictions for other species to adjust for differences in base composition. A software tool named NuPoP is developed in three formats for free download. Conclusions: Simulation studies show that modeling the linker length distribution and utilizing a base composition re-scaling method both improve the prediction of n...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Liqun Xi, Yvonne Fondufe-Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom, Ji-Ping Wang
• Keywords: BMCBI 2010, Nucleosome, Nucleosome Positioning, Software Tool