A Poisson Approximation for Sequence Comparisons with Insertions and Deletions

Abstract

We construct a statistical test for a sequence alignment problem which enables us to decide whether two given sequences are related. Such a test can be used in DNA and protein sequence comparisons. It is based on a comparison of two long sequences of i.i.d. letters taken from a finite alphabet. The test statistic typically employed is the length of the longest matching region between the two sequences in which a certain number of insertions and deletions but no mismatches are allowed. We give a distributional result which enables one to compute $P$-values, and hence to decide whether or not the two sequences are related. Its proof utilizes the Chen-Stein method for Poisson approximation. The test is based on a greedy algorithm that searches for the longest matching region. We show that this algorithm finds the longest matching region with probability approaching 1 as the lengths of the two sequences go to infinity.