on calculating the probability of a set of orthologous

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ON CALCULATING THE PROBABILITY OF A SET OF ORTHOLOGOUS
SEQUENCES
Junfeng Liu1, Liang Chen2, Hongyu Zhao3, Dirk F. Moore1, Yong Lin1 and Weichung
Joe Shih1
1 Biometrics Division, CINJ-UMDNJ, USA, 2 Department of Biological Sciences,
University of Southern California, USA. 3 Department of Epidemiology and Public
Health, Yale University School of Medicine, USA.
ABSTRACT: Probabilistic DNA sequence models have been intensively applied to
genome research. Within the evolutionary biology framework, we investigates the
feasibility for rigorously estimating the probability of a set of orthologous DNA
sequences which evolve from a common progenitor. We propose Monte Carlo integration
algorithms to sample the unknown ancestral and/or root sequences a posteriori
conditional on a reference sequence and apply pairwise Needleman-Wunsch alignment
(1970) between the sampled and non-reference species sequences to estimate the
probability. We apply our algorithms to a set of CREB promoters among Human, Mouse
and Rat.
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