# On expected score of cellwise alignments

Keywords:
longest common subsequence, optimal alignment, large deviation inequality

### Abstract

We consider certain suboptimal alignments of two independent i.i.d. random sequences from a finite alphabet*A*= {1;...,

*K*}, both sequences having length

*n*. In particular, we focus on so-called cellwise alignments, where in the first step so many 1-s as possible are aligned. These aligned 1-s define

*cells*and the rest of the alignment is defined so that the already existing alignment of 1-s remains unchanged. We show that as

*n*grows, for any cellwise alignment, the average score of a cell tends to the expected score of a random cell, a.s. Moreover, we show that a large deviation inequality holds. The second part of the paper is devoted to calculating the expected score of certain cellwise alignment referred to as

*priority letter alignment*. In this alignment, inside every cell first all 2-s are aligned. Then all 3-s are aligned, but in such way that the already existing alignment of 2-s remains unchanged. Then we continue with 4-s and so on. Although easy to describe, for

*K*bigger than 3 the exact formula for expected score is not that straightforward to find. We present a recursive formula for calculating the expected score.

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