JSM 2005 - Toronto

Abstract #304431

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Activity Number: 62
Type: Contributed
Date/Time: Sunday, August 7, 2005 : 4:00 PM to 5:50 PM
Sponsor: Biometrics Section
Abstract - #304431
Title: A Mixture Model in Nucleosome Core DNA Sequence Alignment
Author(s): Ji-Ping Wang*+ and Jonathan Widom
Companies: Northwestern University and BMBCB, Northwestern University
Address: 2006 Sheridan Road, Evanston, 60208, United States
Keywords: DNA sequence alignment ; nucleosome ; mixture model
Abstract:

A well-established fact of natural nucleosome core DNAs is the ~10bp periodicity of some key di-nucleotide signals, including TT, AA, GC ,and TA (Satchwell, Drew, and Travers 1986). We develop a mixture model that characterizes this periodicity probabilistically by assuming a di-nucleotide signal of any type above emits around a series of "hot spots," roughly equally spaced with 10bp, along the core region of a nucleosome, according to a Gaussian distribution. We treated TT and AA as the same, and model the three types of key di-nucleotide signals (TT/AA, GC, and TA) simultaneously allowing phase shift between each. The alignment is optimized over both Watson and Crick strands under the constraint of Palindromic symmetry. The significantly improved alignment of chicken core DNAs confirmed ~10bp periodicity and phase shift properties of the di-nucleotide signals as have been obtained from Fourier analysis. In addition, it reveals that these three di-nucleotide signals are all center-symmetric at position 73.5, where TT/AA and TA signal curves have a trough and GC has a peak.

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