Local alignment of Markov chains (Q862205): Difference between revisions

This paper investigates local alignments without gaps of two independent Markov chains from a finite alphabet. Sufficient conditions are established 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 known results for independent sequences of i.i.d random variables.