Local alignment of Markov chains

Niels Richard Hansen

doi:10.1214/105051606000000321

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Home > Journals > Ann. Appl. Probab. > Volume 16 > Issue 3 > Article

August 2006 Local alignment of Markov chains

Niels Richard Hansen

Ann. Appl. Probab. 16(3): 1262-1296 (August 2006). DOI: 10.1214/105051606000000321

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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. "Local alignment of Markov chains." Ann. Appl. Probab. 16 (3) 1262 - 1296, August 2006. https://doi.org/10.1214/105051606000000321

Information

Published: August 2006

First available in Project Euclid: 2 October 2006

zbMATH: 1113.60054

MathSciNet: MR2260063

Digital Object Identifier: 10.1214/105051606000000321

Subjects:

Primary: 60G70

Secondary: 60F10

Keywords: Chen–Stein method , Extreme value theory , large deviations , local alignment , Markov additive processes , Markov chains , Poisson approximation