Efficient Construction of Generalized Suffix Arrays by Merging Suffix Arrays

We consider constructing the generalized suffix way of strings A and B when the suffix arrays of A and B are given, j.e., merging two suffix arrays of A and B. There are efficient algorithms to merge some special suffix arrays such as the odd array and the even array. However, for the general case that A and B are arbitrary strings, no efficient merging algorithms have been developed. Thus, one had to construct the generalized suffix arrays of A and B by constructing the suffix array of AB from scratch, even though the suffix ways of A and B are given. In this paper, we Present efficient merging algorithms for the suffix arrays of two arbitrary strings A and B drawn from constant and integer alphabets. The experimental results show that merging two suffix ways of A and B are about 5 times faster than constructing the suffix way of AB from scratch for constant alphabets. Our algorithms include searching all suffixes of string B in the suffix array of A. To do this, we use suffix links in suffix ways and we developed efficient algorithms for computing the suffix links. Efficient computation of suffix links is another contribution of this paper because it can be used to solve other problems occurred in bioinformatics that should search all suffixes of a given string in the suffix array of another string such as computing matching statistics, finding longest common substrings, and so on. The experimental results show that our methods for computing suffix links is about 3-4 times faster than the previous fastest methods.