Distribution of Aligned Letter Pairs in Optimal Alignments of Random Sequences
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Publication:6237410
Numerical optimization and variational techniques (65K10) Large deviations (60F10) Asymptotic distribution theory in statistics (62E20) Geometric probability and stochastic geometry (60D05) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Combinatorial optimization (90C27) Combinatorial probability (60C05) Inequalities and extremum problems involving convexity in convex geometry (52A40)
Abstract: Considering the optimal alignment of two i.i.d. random sequences of length , we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges to a unique limiting distribution as tends to infinity. This result is interesting because it helps understanding the microscopic path structure of a special type of last passage percolation problem with correlated weights, an area of long-standing open problems. Characterizing the microscopic path structure yields furthermore a robust alternative to optimal alignment scores for testing the relatedness of genetic sequences.
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