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Local alignment of Markov chains

Niels Richard Hansen
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Abstract

We consider local alignments without gaps of two independent Markov chains from a finite alphabet, and we derive sufficient conditions for the number of essentially different local alignments with a score exceeding a high threshold to be asymptotically Poisson distributed. From the Poisson approximation a Gumbel approximation of the maximal local alignment score is obtained. The results extend those obtained by Dembo, Karlin and Zeitouni [Ann. Probab. 22 (1994) 2022--2039] for independent sequences of i.i.d. variables.

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Niels Richard Hansen. 2006-10-05. Local alignment of Markov chains. https://doi.org/10.1214/105051606000000321

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