Local alignment of Markov chains

Details Local alignment of Markov chains Local alignment of Markov chains

2006-10-05

arxiv.org/abs/math/0610187v1

Annals of Applied Probability 2006, Vol. 16, No. 3, 1262-1296

Mathematics

Probability

Published at http://dx.doi.org/10.1214/105051606000000321 in the Annals of Applied Probability (http://www.imstat.org/aap/) by

Scientific paper

10.1214/105051606000000321

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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