On the Variance of the Optimal Alignment Score for an Asymmetric Scoring Function

Details On the Variance of the Optimal Alignment Score for an Asymmetric Scoring Function On the Variance of the Optimal Alignment Score for an Asymmetric Scoring Function

2007-02-01

arxiv.org/abs/math/0702036v2

Mathematics

Probability

39 pages. A statement of a theorem in the old text truncated and so non understandable

Scientific paper

We investigate the variance of the optimal alignment score of two independent
iid binary, with parameter 1/2, sequences of length $n$. The scoring function
is such that one letter has a somewhat larger score than the other letter. In
this setting, we prove that the variance is of order $n$, and this confirms
Waterman's conjecture in this case.

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