The Mathematical Institute, University of Oxford, Eprints Archive

Distribution of Aligned Letter Pairs in Optimal Alignments of Random Sequences

Hauser, Raphael and Matzinger, Heinrich (2012) Distribution of Aligned Letter Pairs in Optimal Alignments of Random Sequences. Technical Report. Annals of Probability. (Submitted)

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Abstract

Considering the optimal alignment of two i.i.d. random sequences of length $n$, 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 $n$ 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.

Item Type:Technical Report (Technical Report)
Subjects:O - Z > Statistics
O - Z > Operations research, mathematical programming
A - C > Convex and discrete geometry
O - Z > Probability theory and stochastic processes
H - N > Numerical analysis
Research Groups:Numerical Analysis Group
ID Code:1625
Deposited By:Lotti Ekert
Deposited On:24 Nov 2012 08:57
Last Modified:24 Nov 2012 08:57

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