The Annals of Applied Probability

Local alignment of Markov chains

Niels Richard Hansen

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.

Article information

Source
Ann. Appl. Probab., Volume 16, Number 3 (2006), 1262-1296.

Dates
First available in Project Euclid: 2 October 2006

https://projecteuclid.org/euclid.aoap/1159804981

Digital Object Identifier
doi:10.1214/105051606000000321

Mathematical Reviews number (MathSciNet)
MR2260063

Zentralblatt MATH identifier
1113.60054

Subjects
Primary: 60G70: Extreme value theory; extremal processes
Secondary: 60F10: Large deviations

Citation

Hansen, Niels Richard. Local alignment of Markov chains. Ann. Appl. Probab. 16 (2006), no. 3, 1262--1296. doi:10.1214/105051606000000321. https://projecteuclid.org/euclid.aoap/1159804981

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